3-122183002-G-A

Variant names:

• chr3-122183002-G-A
• rs6776158

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.612 in 152,010 control chromosomes in the GnomAD database, including 28,784 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.61 (28784 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.16
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 3-122183002-G-A is Benign according to our data. Variant chr3-122183002-G-A is described in ClinVar as Benign. ClinVar VariationId is 1167241.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92881 AN: 151890 Hom.: 28752 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.612 AC: 92961 AN: 152010 Hom.: 28784 Cov.: 33 AF XY: 0.611 AC XY: 45397 AN XY: 74298

African (AFR) AF: 0.580 AC: 24032 AN: 41446

American (AMR) AF: 0.738 AC: 11287 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1930 AN: 5170

South Asian (SAS) AF: 0.464 AC: 2231 AN: 4810

European-Finnish (FIN) AF: 0.574 AC: 6049 AN: 10536

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43144 AN: 67966

Other (OTH) AF: 0.624 AC: 1315 AN: 2108

Alfa AF: 0.616 Hom.: 13001

Bravo AF: 0.625

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autosomal dominant hypocalcemia 1;C1809471:Familial hypocalciuric hypercalcemia Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.34
DANN	Benign	0.59
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6776158; hg19: chr3-121901849;