rs11739623

Positions:

• chr5-132528460-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 0.194 in 152,170 control chromosomes in the GnomAD database, including 3,425 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 0.19 (3425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.194 AC: 29571 AN: 152052 Hom.: 3423 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.194 AC: 29576 AN: 152170 Hom.: 3425 Cov.: 32 AF XY: 0.192 AC XY: 14276 AN XY: 74408

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.233

Alfa AF: 0.244 Hom.: 7796

Bravo AF: 0.189

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
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: rs11739623; hg19: chr5-131864152; COSMIC: COSV60199142;