5-132673462-C-T

Position:

• chr5-132673462-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;