rs949602

Variant names:

• chr5-157963832-A-C
• rs949602

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 0.591 in 152,030 control chromosomes in the GnomAD database, including 26,929 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 0.59 (26929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.591 AC: 89841 AN: 151910 Hom.: 26916 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.591 AC: 89902 AN: 152030 Hom.: 26929 Cov.: 32 AF XY: 0.589 AC XY: 43789 AN XY: 74318

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.566

Alfa AF: 0.574 Hom.: 37859

Bravo AF: 0.599

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.39
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs949602; hg19: chr5-157390840;