5-132673462-C-T

Variant names:

• chr5-132673462-C-T
• rs2243250

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.35 (13170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 5-132673462-C-T is Benign according to our data. Variant chr5-132673462-C-T is described in Lovd as [Benign].
• 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

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.298

Alfa AF: 0.185 Hom.: 4307

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243250; hg19: chr5-132009154;