rs2961720

Variant names:

• chr5-142200665-G-A
• rs2961720

Your query was ambiguous. Multiple possible variants found:

• chr5-142200665-G-A
• chr5-142200665-G-C
• chr5-142200665-G-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 0.923 in 152,168 control chromosomes in the GnomAD database, including 64,980 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 0.92 (64980 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 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: 0.923 AC: 140349 AN: 152050 Hom.: 64914 Cov.: 30

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.923 AC: 140474 AN: 152168 Hom.: 64980 Cov.: 30 AF XY: 0.923 AC XY: 68634 AN XY: 74382

African (AFR) AF: 0.981 AC: 40742 AN: 41520

American (AMR) AF: 0.930 AC: 14204 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4798 AN: 5160

South Asian (SAS) AF: 0.891 AC: 4289 AN: 4816

European-Finnish (FIN) AF: 0.920 AC: 9748 AN: 10594

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60804 AN: 68010

Other (OTH) AF: 0.904 AC: 1912 AN: 2114

Alfa AF: 0.897 Hom.: 30967

Bravo AF: 0.928

Asia WGS AF: 0.936 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs2961720; hg19: chr5-141580230;