chr3-70879779-A-C

Variant names:

• chr3-70879779-A-C
• rs2687201

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 0.576 in 151,996 control chromosomes in the GnomAD database, including 27,390 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 0.58 (27390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.697 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: 0.577 AC: 87586 AN: 151878 Hom.: 27384 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.576 AC: 87619 AN: 151996 Hom.: 27390 Cov.: 32 AF XY: 0.581 AC XY: 43134 AN XY: 74300

African (AFR) AF: 0.312 AC: 12919 AN: 41446

American (AMR) AF: 0.687 AC: 10496 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2774 AN: 5150

South Asian (SAS) AF: 0.717 AC: 3450 AN: 4812

European-Finnish (FIN) AF: 0.674 AC: 7125 AN: 10570

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46385 AN: 67968

Other (OTH) AF: 0.613 AC: 1290 AN: 2106

Alfa AF: 0.650 Hom.: 127808

Bravo AF: 0.563

Asia WGS AF: 0.617 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2687201; hg19: chr3-70928930; COSMIC: COSV68613907;