rs715271

Variant names:

• chr2-56906275-C-A
• rs715271

Your query was ambiguous. Multiple possible variants found:

• chr2-56906275-C-A
• chr2-56906275-C-G
• chr2-56906275-C-T

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 0.631 in 151,864 control chromosomes in the GnomAD database, including 30,963 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 0.63 (30963 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 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: 0.631 AC: 95729 AN: 151746 Hom.: 30950 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.631 AC: 95768 AN: 151864 Hom.: 30963 Cov.: 31 AF XY: 0.628 AC XY: 46626 AN XY: 74206

African (AFR) AF: 0.534 AC: 22111 AN: 41416

American (AMR) AF: 0.559 AC: 8514 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2231 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1888 AN: 5146

South Asian (SAS) AF: 0.617 AC: 2972 AN: 4814

European-Finnish (FIN) AF: 0.736 AC: 7770 AN: 10562

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.709 AC: 48149 AN: 67910

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.672 Hom.: 12047

Bravo AF: 0.611

Asia WGS AF: 0.518 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.26
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs715271; hg19: chr2-57133410;