3-156618766-C-T

Variant names:

• chr3-156618766-C-T
• rs7651778

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 0.399 in 151,860 control chromosomes in the GnomAD database, including 13,717 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 0.40 (13717 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60545 AN: 151742 Hom.: 13711 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.399 AC: 60551 AN: 151860 Hom.: 13717 Cov.: 31 AF XY: 0.400 AC XY: 29714 AN XY: 74194

African (AFR) AF: 0.178 AC: 7388 AN: 41406

American (AMR) AF: 0.520 AC: 7932 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3257 AN: 5162

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4820

European-Finnish (FIN) AF: 0.428 AC: 4492 AN: 10506

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32697 AN: 67944

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.446 Hom.: 34692

Bravo AF: 0.400

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.66
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs7651778; hg19: chr3-156336555;