chr3-120675486-AATGCTCACATCCATGGTGTTCAAGGGGAATATGAGGGATTCTCTTTAACTCTGGATTTTTGGGGATCCTACTGGAAACCCTACAGTTAATTTCACTAGTTTGGATTGGCTGCTGTGCCACCAATCCAATTTTAATCTTTGTGTTGTCATTGCTCTGTATCTTCATTGCCCCTATGACTTGGGAAACCTCTAGACAGTTCACAGGCTAGATTGGAAGAGCCACGGTGGGTGGAGGCACTTTGGCCTGAAAGCTAGTCATCCAGGAATAGGATTCAGAGCTCTTCTAAGCACTTTATTTGCTCATACCTGTCCTTCTGGCAGGGAACCTGGGCAGCGAGGATCCTCTGAAGAACACTCATTCCCAAATCCAGAAATGTACTGTAGGTGACAAAGACACAAATGCCACCATTAGCAGGATTTAAAGAGCATTTCAGAAAATTGGCAGTTTACTAAGGTAAGAATTTCTATATGGACCTATGTTTGTGTATGATGTTCCACATATAATATCTTTACTGTGTCTTGACATATGAATCATTTAGGGAAGACAATATGGTTTCTGTGAATTTTAAAGACTTCTAATTAATCAGAAGAGTGCTGGATATTGCATAGACTTCTCCACCCTTAGCTGTACTTAGCTGATTTGTGGGTCT-A

Variant names:

• chr3-120675486-AATGCTCACATCCATGGTGTTCAAGGGGAATATGAGGGATTCTCTTTAACTCTGGATTTTTGGGGATCCTACTGGAAACCCTACAGTTAATTTCACTAGTTTGGATTGGCTGCTGTGCCACCAATCCAATTTTAATCTTTGTGTTGTCATTGCTCTGTATCTTCATTGCCCCTATGACTTGGGAAACCTCTAGACAGTTCACAGGCTAGATTGGAAGAGCCACGGTGGGTGGAGGCACTTTGGCCTGAAAGCTAGTCATCCAGGAATAGGATTCAGAGCTCTTCTAAGCACTTTATTTGCTCATACCTGTCCTTCTGGCAGGGAACCTGGGCAGCGAGGATCCTCTGAAGAACACTCATTCCCAAATCCAGAAATGTACTGTAGGTGACAAAGACACAAATGCCACCATTAGCAGGATTTAAAGAGCATTTCAGAAAATTGGCAGTTTACTAAGGTAAGAATTTCTATATGGACCTATGTTTGTGTATGATGTTCCACATATAATATCTTTACTGTGTCTTGACATATGAATCATTTAGGGAAGACAATATGGTTTCTGTGAATTTTAAAGACTTCTAATTAATCAGAAGAGTGCTGGATATTGCATAGACTTCTCCACCCTTAGCTGTACTTAGCTGATTTGTGGGTCT-A
• rs1553721650
• NM_000187.4:c.16-272_87+305del

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PVS1_Moderate PP5

The NM_000187.4(HGD):​c.16-272_87+305del variant causes a exon loss, splice acceptor, splice donor, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: HGD NM_000187.4 exon_loss, splice_acceptor, splice_donor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 0.666
• Publications: 1 publications found

Genes affected

HGD (HGNC:4892): (homogentisate 1,2-dioxygenase) This gene encodes the enzyme homogentisate 1,2 dioxygenase. This enzyme is involved in the catabolism of the amino acids tyrosine and phenylalanine. Mutations in this gene are the cause of the autosomal recessive metabolism disorder alkaptonuria.[provided by RefSeq, May 2010]

HGD Gene-Disease associations (from GenCC):

• alkaptonuria

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.05381166 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PP5: Variant 3-120675486-AATGCTCACATCCATGGTGTTCAAGGGGAATATGAGGGATTCTCTTTAACTCTGGATTTTTGGGGATCCTACTGGAAACCCTACAGTTAATTTCACTAGTTTGGATTGGCTGCTGTGCCACCAATCCAATTTTAATCTTTGTGTTGTCATTGCTCTGTATCTTCATTGCCCCTATGACTTGGGAAACCTCTAGACAGTTCACAGGCTAGATTGGAAGAGCCACGGTGGGTGGAGGCACTTTGGCCTGAAAGCTAGTCATCCAGGAATAGGATTCAGAGCTCTTCTAAGCACTTTATTTGCTCATACCTGTCCTTCTGGCAGGGAACCTGGGCAGCGAGGATCCTCTGAAGAACACTCATTCCCAAATCCAGAAATGTACTGTAGGTGACAAAGACACAAATGCCACCATTAGCAGGATTTAAAGAGCATTTCAGAAAATTGGCAGTTTACTAAGGTAAGAATTTCTATATGGACCTATGTTTGTGTATGATGTTCCACATATAATATCTTTACTGTGTCTTGACATATGAATCATTTAGGGAAGACAATATGGTTTCTGTGAATTTTAAAGACTTCTAATTAATCAGAAGAGTGCTGGATATTGCATAGACTTCTCCACCCTTAGCTGTACTTAGCTGATTTGTGGGTCT-A is Pathogenic according to our data. Variant chr3-120675486-AATGCTCACATCCATGGTGTTCAAGGGGAATATGAGGGATTCTCTTTAACTCTGGATTTTTGGGGATCCTACTGGAAACCCTACAGTTAATTTCACTAGTTTGGATTGGCTGCTGTGCCACCAATCCAATTTTAATCTTTGTGTTGTCATTGCTCTGTATCTTCATTGCCCCTATGACTTGGGAAACCTCTAGACAGTTCACAGGCTAGATTGGAAGAGCCACGGTGGGTGGAGGCACTTTGGCCTGAAAGCTAGTCATCCAGGAATAGGATTCAGAGCTCTTCTAAGCACTTTATTTGCTCATACCTGTCCTTCTGGCAGGGAACCTGGGCAGCGAGGATCCTCTGAAGAACACTCATTCCCAAATCCAGAAATGTACTGTAGGTGACAAAGACACAAATGCCACCATTAGCAGGATTTAAAGAGCATTTCAGAAAATTGGCAGTTTACTAAGGTAAGAATTTCTATATGGACCTATGTTTGTGTATGATGTTCCACATATAATATCTTTACTGTGTCTTGACATATGAATCATTTAGGGAAGACAATATGGTTTCTGTGAATTTTAAAGACTTCTAATTAATCAGAAGAGTGCTGGATATTGCATAGACTTCTCCACCCTTAGCTGTACTTAGCTGATTTGTGGGTCT-A is described in ClinVar as Pathogenic. ClinVar VariationId is 156275.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HGD	NM_000187.4	c.16-272_87+305del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 2 of 14	ENST00000283871.10	NP_000178.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HGD	ENST00000283871.10	c.16-272_87+305del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 2 of 14	1	NM_000187.4	ENSP00000283871.5

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

Submissions by phenotype

Alkaptonuria Pathogenic:2

-

Chehab Lab, University of California, San Francisco

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

-

Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

The variant was originally described in PMID:25233259. It has been submitted to the HGD gene mutation database (http://hgddatabase.cvtisr.sk/, DB-ID: AKU_00164). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1553721650; hg19: chr3-120394333;