rs952008

Variant names:

• chr4-171346736-T-C
• rs952008

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 0.616 in 151,854 control chromosomes in the GnomAD database, including 31,434 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 0.62 (31434 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 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: 0.616 AC: 93484 AN: 151736 Hom.: 31424 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.616 AC: 93533 AN: 151854 Hom.: 31434 Cov.: 31 AF XY: 0.615 AC XY: 45613 AN XY: 74208

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.626

Alfa AF: 0.740 Hom.: 39855

Bravo AF: 0.587

Asia WGS AF: 0.560 AC: 1945 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952008; hg19: chr4-172267887;