rs6459961

Variant names:

• chr7-155905561-C-A
• rs6459961

Your query was ambiguous. Multiple possible variants found:

• chr7-155905561-C-A
• chr7-155905561-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 151,972 control chromosomes in the GnomAD database, including 30,540 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 (30540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 6 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 = 0.643 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: 95848 AN: 151854 Hom.: 30536 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.631 AC: 95879 AN: 151972 Hom.: 30540 Cov.: 32 AF XY: 0.629 AC XY: 46688 AN XY: 74246

African (AFR) AF: 0.650 AC: 26930 AN: 41432

American (AMR) AF: 0.523 AC: 7984 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2650 AN: 3468

East Asian (EAS) AF: 0.630 AC: 3250 AN: 5158

South Asian (SAS) AF: 0.609 AC: 2929 AN: 4806

European-Finnish (FIN) AF: 0.625 AC: 6590 AN: 10542

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43503 AN: 67976

Other (OTH) AF: 0.626 AC: 1321 AN: 2110

Alfa AF: 0.641 Hom.: 142193

Bravo AF: 0.624

Asia WGS AF: 0.601 AC: 2088 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	1.7
DANN	Benign	0.47
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6459961; hg19: chr7-155698255;