rs959960

Positions:

• chr3-160751268-T-C

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 0.546 in 151,930 control chromosomes in the GnomAD database, including 25,797 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 0.55 (25797 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82848 AN: 151812 Hom.: 25741 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.546 AC: 82963 AN: 151930 Hom.: 25797 Cov.: 31 AF XY: 0.541 AC XY: 40205 AN XY: 74260

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.497

Alfa AF: 0.426 Hom.: 17450

Bravo AF: 0.575

Asia WGS AF: 0.567 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959960; hg19: chr3-160469056;