5-51356860-T-C

Variant names:

• chr5-51356860-T-C
• rs6867206

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 0.481 in 152,058 control chromosomes in the GnomAD database, including 19,153 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 0.48 (19153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.480 AC: 73007 AN: 151940 Hom.: 19114 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.481 AC: 73105 AN: 152058 Hom.: 19153 Cov.: 32 AF XY: 0.474 AC XY: 35231 AN XY: 74328

African (AFR) AF: 0.685 AC: 28433 AN: 41478

American (AMR) AF: 0.376 AC: 5740 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3470

East Asian (EAS) AF: 0.158 AC: 814 AN: 5160

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4889 AN: 10572

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29047 AN: 67984

Other (OTH) AF: 0.439 AC: 924 AN: 2104

Alfa AF: 0.438 Hom.: 7511

Bravo AF: 0.480

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6867206; hg19: chr5-50652694;