5-5876510-T-C

Variant names:

• chr5-5876510-T-C
• rs950651

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 0.815 in 152,130 control chromosomes in the GnomAD database, including 50,558 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 0.81 (50558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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 (SAS) allele frequency at 95% confidence interval = 0.851 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: 0.815 AC: 123853 AN: 152012 Hom.: 50551 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.815 AC: 123910 AN: 152130 Hom.: 50558 Cov.: 32 AF XY: 0.814 AC XY: 60501 AN XY: 74364

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.782

Alfa AF: 0.805 Hom.: 22696

Bravo AF: 0.822

Asia WGS AF: 0.794 AC: 2759 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	0.41
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950651; hg19: chr5-5876623;