chr3-122183002-G-A

Position:

• chr3-122183002-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.624

Alfa AF: 0.614 Hom.: 11299

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

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6776158; hg19: chr3-121901849;