5-51136344-T-C

Variant names:

• chr5-51136344-T-C
• rs2962271

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.926 AC: 38434 AN: 41490

American (AMR) AF: 0.913 AC: 13920 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3155 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5146 AN: 5172

South Asian (SAS) AF: 0.950 AC: 4568 AN: 4810

European-Finnish (FIN) AF: 0.935 AC: 9899 AN: 10588

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60261 AN: 67998

Other (OTH) AF: 0.900 AC: 1899 AN: 2110

Alfa AF: 0.894 Hom.: 102316

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs2962271; hg19: chr5-50432178;