5-51136344-T-C

Variant names:

• chr5-51136344-T-C
• rs2962271

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 0.91 in 152,094 control chromosomes in the GnomAD database, including 63,025 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 0.91 (63025 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.910 AC: 138226 AN: 151980 Hom.: 62970 Cov.: 30

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.910 AC: 138336 AN: 152094 Hom.: 63025 Cov.: 30 AF XY: 0.914 AC XY: 67903 AN XY: 74318

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.900

Alfa AF: 0.893 Hom.: 80753

Bravo AF: 0.909

Asia WGS AF: 0.951 AC: 3307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.3
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: rs2962271; hg19: chr5-50432178;