5-132673462-C-T

Variant names:

• chr5-132673462-C-T
• rs2243250

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 0.347 in 151,970 control chromosomes in the GnomAD database, including 13,170 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 0.35 (13170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 833 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.347 AC: 52630 AN: 151852 Hom.: 13140 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.347 AC: 52718 AN: 151970 Hom.: 13170 Cov.: 32 AF XY: 0.354 AC XY: 26257 AN XY: 74256

African (AFR) AF: 0.651 AC: 26964 AN: 41392

American (AMR) AF: 0.341 AC: 5204 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.775 AC: 4006 AN: 5172

South Asian (SAS) AF: 0.188 AC: 904 AN: 4818

European-Finnish (FIN) AF: 0.359 AC: 3783 AN: 10550

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10312 AN: 67974

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.226 Hom.: 17877

Bravo AF: 0.367

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.96
DANN	Benign	0.60
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2243250; hg19: chr5-132009154;