3-122295719-T-C

Variant names:

• chr3-122295719-T-C
• rs13083990

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.306 in 152,038 control chromosomes in the GnomAD database, including 8,390 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8390 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46553 AN: 151920 Hom.: 8377 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.306 AC: 46591 AN: 152038 Hom.: 8390 Cov.: 31 AF XY: 0.311 AC XY: 23131 AN XY: 74332

African (AFR) AF: 0.128 AC: 5310 AN: 41486

American (AMR) AF: 0.407 AC: 6219 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1867 AN: 3466

East Asian (EAS) AF: 0.557 AC: 2877 AN: 5162

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4816

European-Finnish (FIN) AF: 0.318 AC: 3356 AN: 10568

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23388 AN: 67958

Other (OTH) AF: 0.363 AC: 767 AN: 2114

Alfa AF: 0.342 Hom.: 24087

Bravo AF: 0.306

Asia WGS AF: 0.527 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.45
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs13083990; hg19: chr3-122014566;