rs743562

Variant names:

• chr5-132536691-C-T
• rs743562
• ENST00000638452.2:c.-168-22593C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638452.2(ENSG00000283782):​c.-168-22593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 27 publications found

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000638452.2	c.-168-22593C>T		intron_variant	Intron 3 of 26	5		ENSP00000492349.2

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

African (AFR) AF: 0.186 AC: 7728 AN: 41446

American (AMR) AF: 0.314 AC: 4796 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2523 AN: 5162

South Asian (SAS) AF: 0.407 AC: 1956 AN: 4810

European-Finnish (FIN) AF: 0.444 AC: 4686 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29476 AN: 67954

Other (OTH) AF: 0.386 AC: 817 AN: 2116

Alfa AF: 0.402 Hom.: 22025

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

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