rs4960563

Variant names:

• chr7-154903843-T-C
• rs4960563

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 0.763 in 151,996 control chromosomes in the GnomAD database, including 44,524 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 0.76 (44524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115798 AN: 151880 Hom.: 44476 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.763 AC: 115908 AN: 151996 Hom.: 44524 Cov.: 32 AF XY: 0.758 AC XY: 56282 AN XY: 74278

African (AFR) AF: 0.873 AC: 36210 AN: 41484

American (AMR) AF: 0.736 AC: 11249 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2394 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3808 AN: 5140

South Asian (SAS) AF: 0.691 AC: 3338 AN: 4832

European-Finnish (FIN) AF: 0.697 AC: 7332 AN: 10524

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49141 AN: 67956

Other (OTH) AF: 0.738 AC: 1559 AN: 2112

Alfa AF: 0.733 Hom.: 77548

Bravo AF: 0.771

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.17
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4960563; hg19: chr7-154695553;