rs6461625

Variant names:

• chr7-21960807-G-A
• rs6461625

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 0.561 in 148,918 control chromosomes in the GnomAD database, including 23,719 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 0.56 (23719 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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: 0.561 AC: 83421 AN: 148800 Hom.: 23712 Cov.: 24

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.561 AC: 83469 AN: 148918 Hom.: 23719 Cov.: 24 AF XY: 0.562 AC XY: 40630 AN XY: 72344

African (AFR) AF: 0.613 AC: 24749 AN: 40370

American (AMR) AF: 0.531 AC: 7904 AN: 14880

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1803 AN: 3462

East Asian (EAS) AF: 0.427 AC: 2116 AN: 4954

South Asian (SAS) AF: 0.401 AC: 1882 AN: 4690

European-Finnish (FIN) AF: 0.631 AC: 6168 AN: 9770

Middle Eastern (MID) AF: 0.563 AC: 162 AN: 288

European-Non Finnish (NFE) AF: 0.548 AC: 37024 AN: 67534

Other (OTH) AF: 0.538 AC: 1111 AN: 2066

Alfa AF: 0.548 Hom.: 101663

Bravo AF: 0.562

Asia WGS AF: 0.426 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs6461625; hg19: chr7-22000425;