rs963251

chr4-115247081-C-Gchr4-115247081-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 0.578 in 149,826 control chromosomes in the GnomAD database, including 28,475 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 0.58 (28475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.579 AC: 86627 AN: 149710 Hom.: 28464 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.556

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.578 AC: 86660 AN: 149826 Hom.: 28475 Cov.: 30 AF XY: 0.578 AC XY: 42292 AN XY: 73114

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.596

Alfa AF: 0.599 Hom.: 3126

Bravo AF: 0.571

Asia WGS AF: 0.561 AC: 1932 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963251; hg19: chr4-116168237;