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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: 15-45366179-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=45366179&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2_Supporting",
"PS3_Supporting"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GATM",
"hgnc_id": 4175,
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"inheritance_mode": "AD,AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001482.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2_Supporting,PS3_Supporting",
"acmg_score": 2,
"allele_count_reference_population": 16,
"alphamissense_prediction": null,
"alphamissense_score": 0.158,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.04,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Arginine:glycine amidinotransferase deficiency,Fanconi renotubular syndrome 1,Inborn genetic diseases,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "LP:1 US:4",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7097145915031433,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 423,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2348,
"cdna_start": 936,
"cds_end": null,
"cds_length": 1272,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001482.3",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000396659.8",
"protein_coding": true,
"protein_id": "NP_001473.1",
"strand": false,
"transcript": "NM_001482.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 423,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2348,
"cdna_start": 936,
"cds_end": null,
"cds_length": 1272,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000396659.8",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001482.3",
"protein_coding": true,
"protein_id": "ENSP00000379895.3",
"strand": false,
"transcript": "ENST00000396659.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3911,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000558362.5",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "n.2501G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000558362.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 432,
"aa_ref": "R",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2367,
"cdna_start": 963,
"cds_end": null,
"cds_length": 1299,
"cds_start": 872,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887717.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.872G>A",
"hgvs_p": "p.Arg291His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557776.1",
"strand": false,
"transcript": "ENST00000887717.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 429,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2364,
"cdna_start": 936,
"cds_end": null,
"cds_length": 1290,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887714.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557773.1",
"strand": false,
"transcript": "ENST00000887714.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 421,
"aa_ref": "R",
"aa_start": 280,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2341,
"cdna_start": 931,
"cds_end": null,
"cds_length": 1266,
"cds_start": 839,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887712.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.839G>A",
"hgvs_p": "p.Arg280His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557771.1",
"strand": false,
"transcript": "ENST00000887712.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 405,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2293,
"cdna_start": 937,
"cds_end": null,
"cds_length": 1218,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887711.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557770.1",
"strand": false,
"transcript": "ENST00000887711.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 403,
"aa_ref": "R",
"aa_start": 262,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1909,
"cdna_start": 1046,
"cds_end": null,
"cds_length": 1212,
"cds_start": 785,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000675701.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Arg262His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502671.1",
"strand": false,
"transcript": "ENST00000675701.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 403,
"aa_ref": "R",
"aa_start": 262,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2286,
"cdna_start": 877,
"cds_end": null,
"cds_length": 1212,
"cds_start": 785,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887713.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Arg262His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557772.1",
"strand": false,
"transcript": "ENST00000887713.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1522,
"cdna_start": 939,
"cds_end": null,
"cds_length": 1176,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000558336.5",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000454008.1",
"strand": false,
"transcript": "ENST00000558336.5",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3964,
"cdna_start": 936,
"cds_end": null,
"cds_length": 1176,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000675323.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502445.1",
"strand": false,
"transcript": "ENST00000675323.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 384,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2229,
"cdna_start": 937,
"cds_end": null,
"cds_length": 1155,
"cds_start": 845,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000887715.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.845G>A",
"hgvs_p": "p.Arg282His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557774.1",
"strand": false,
"transcript": "ENST00000887715.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 377,
"aa_ref": "R",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2207,
"cdna_start": 798,
"cds_end": null,
"cds_length": 1134,
"cds_start": 707,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000887716.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.707G>A",
"hgvs_p": "p.Arg236His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000557775.1",
"strand": false,
"transcript": "ENST00000887716.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 294,
"aa_ref": "R",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2804,
"cdna_start": 1392,
"cds_end": null,
"cds_length": 885,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001321015.2",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001307944.1",
"strand": false,
"transcript": "NM_001321015.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 476,
"aa_ref": "R",
"aa_start": 335,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4012,
"cdna_start": 2600,
"cds_end": null,
"cds_length": 1431,
"cds_start": 1004,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047432385.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.1004G>A",
"hgvs_p": "p.Arg335His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288341.1",
"strand": false,
"transcript": "XM_047432385.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 439,
"aa_ref": "R",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2814,
"cdna_start": 1402,
"cds_end": null,
"cds_length": 1320,
"cds_start": 893,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047432386.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.893G>A",
"hgvs_p": "p.Arg298His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288342.1",
"strand": false,
"transcript": "XM_047432386.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 439,
"aa_ref": "R",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2774,
"cdna_start": 1362,
"cds_end": null,
"cds_length": 1320,
"cds_start": 893,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047432387.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.893G>A",
"hgvs_p": "p.Arg298His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288343.1",
"strand": false,
"transcript": "XM_047432387.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 294,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2613,
"cdna_start": 1201,
"cds_end": null,
"cds_length": 885,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047432388.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288344.1",
"strand": false,
"transcript": "XM_047432388.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 913,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000558916.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "n.743G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000558916.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2051,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000674905.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "n.845G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502176.1",
"strand": false,
"transcript": "ENST00000674905.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2142,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000675158.1",
"gene_hgnc_id": 4175,
"gene_symbol": "GATM",
"hgvs_c": "n.845G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
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],
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"phenotype_combined": "not provided|Arginine:glycine amidinotransferase deficiency|Inborn genetic diseases|Arginine:glycine amidinotransferase deficiency;Fanconi renotubular syndrome 1",
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]
}