rs2687201

Variant names:

• chr3-70879779-A-C
• rs2687201

Your query was ambiguous. Multiple possible variants found:

• chr3-70879779-A-C
• chr3-70879779-A-G
• chr3-70879779-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.613

Alfa AF: 0.664 Hom.: 56642

Bravo AF: 0.563

Asia WGS AF: 0.617 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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