rs4960563

Variant names:

• chr7-154903843-T-C
• rs4960563

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 0.763 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.762 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

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.738

Alfa AF: 0.727 Hom.: 55436

Bravo AF: 0.771

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4960563; hg19: chr7-154695553;