rs7561317

Variant names:

• chr2-644953-A-G
• rs7561317

Your query was ambiguous. Multiple possible variants found:

• chr2-644953-A-G
• chr2-644953-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 0.817 in 152,184 control chromosomes in the GnomAD database, including 50,952 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 0.82 (50952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -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 = 0.897 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: 0.817 AC: 124264 AN: 152066 Hom.: 50931 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.817 AC: 124340 AN: 152184 Hom.: 50952 Cov.: 33 AF XY: 0.821 AC XY: 61067 AN XY: 74422

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.827

Alfa AF: 0.822 Hom.: 71868

Bravo AF: 0.814

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7561317; hg19: chr2-644953;