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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.626

Alfa AF: 0.646 Hom.: 67295

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6459961; hg19: chr7-155698255;