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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: X-78014478-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78014478&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78014478,
"ref": "G",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000341514.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "NM_000052.7",
"protein_id": "NP_000043.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1500,
"cds_start": -4,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "ENST00000341514.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000341514.11",
"protein_id": "ENSP00000345728.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1500,
"cds_start": -4,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "NM_000052.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2500-184G>T",
"hgvs_p": null,
"transcript": "ENST00000689767.1",
"protein_id": "ENSP00000509406.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1531,
"cds_start": -4,
"cds_end": null,
"cds_length": 4596,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2437-184G>T",
"hgvs_p": null,
"transcript": "ENST00000343533.10",
"protein_id": "ENSP00000343026.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1510,
"cds_start": -4,
"cds_end": null,
"cds_length": 4533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000685264.1",
"protein_id": "ENSP00000510136.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1500,
"cds_start": -4,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000686133.1",
"protein_id": "ENSP00000509233.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1500,
"cds_start": -4,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000687086.1",
"protein_id": "ENSP00000509566.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1500,
"cds_start": -4,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000686033.1",
"protein_id": "ENSP00000510693.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1435,
"cds_start": -4,
"cds_end": null,
"cds_length": 4308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2173-184G>T",
"hgvs_p": null,
"transcript": "NM_001282224.2",
"protein_id": "NP_001269153.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1422,
"cds_start": -4,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2173-184G>T",
"hgvs_p": null,
"transcript": "ENST00000686543.1",
"protein_id": "ENSP00000509477.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1422,
"cds_start": -4,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2173-184G>T",
"hgvs_p": null,
"transcript": "ENST00000692908.1",
"protein_id": "ENSP00000508627.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1422,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 16,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000689530.1",
"protein_id": "ENSP00000509707.1",
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000686688.1",
"protein_id": "ENSP00000509416.1",
"transcript_support_level": null,
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},
{
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"strand": true,
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],
"exon_rank": null,
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"exon_count": 13,
"intron_rank": 10,
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"gene_symbol": "ATP7A",
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"hgvs_c": "c.2407-184G>T",
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"transcript": "ENST00000693398.1",
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},
{
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],
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"exon_count": 11,
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"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null,
"transcript": "ENST00000689649.1",
"protein_id": "ENSP00000509277.1",
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
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"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2173-184G>T",
"hgvs_p": null,
"transcript": "ENST00000686480.1",
"protein_id": "ENSP00000508978.1",
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},
{
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],
"exon_rank": null,
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"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.-19-95389G>T",
"hgvs_p": null,
"transcript": "ENST00000644362.1",
"protein_id": "ENSP00000496140.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.*2321-184G>T",
"hgvs_p": null,
"transcript": "ENST00000645094.1",
"protein_id": "ENSP00000493605.1",
"transcript_support_level": null,
"aa_start": null,
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"mane_select": null,
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 14,
"intron_rank": 1,
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"gene_symbol": "ATP7A",
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"hgvs_c": "n.824-184G>T",
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},
{
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"strand": true,
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],
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"intron_rank": 2,
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"gene_symbol": "ATP7A",
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},
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],
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"gene_symbol": "ATP7A",
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"hgvs_c": "n.449-184G>T",
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},
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.*356-184G>T",
"hgvs_p": null,
"transcript": "ENST00000689872.1",
"protein_id": "ENSP00000509373.1",
"transcript_support_level": null,
"aa_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.285-16922G>T",
"hgvs_p": null,
"transcript": "NR_104109.2",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
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},
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"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.-184G>T",
"hgvs_p": null,
"transcript": "ENST00000685033.1",
"protein_id": "ENSP00000509269.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 588,
"cds_start": -4,
"cds_end": null,
"cds_length": 1767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.*41G>T",
"hgvs_p": null,
"transcript": "ENST00000688746.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"dbsnp": "rs5959964",
"frequency_reference_population": 0.26423168,
"hom_count_reference_population": 11642,
"allele_count_reference_population": 29205,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.264232,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 29205,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 3028,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8299999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.86,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000341514.11",
"gene_symbol": "ATP7A",
"hgnc_id": 869,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.2407-184G>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000644362.1",
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-19-95389G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}