rs743562

chr5-132536691-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.356 in 151,966 control chromosomes in the GnomAD database, including 10,682 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 0.36 (10682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54091 AN: 151848 Hom.: 10676 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.356 AC: 54106 AN: 151966 Hom.: 10682 Cov.: 31 AF XY: 0.355 AC XY: 26397 AN XY: 74264

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.386

Alfa AF: 0.409 Hom.: 18131

Bravo AF: 0.339

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.15
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs743562; hg19: chr5-131872383; COSMIC: COSV51504388; COSMIC: COSV51504388;