rs11747728

chr5-175436499-A-G

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 0.135 in 152,186 control chromosomes in the GnomAD database, including 1,481 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 0.13 (1481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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: 0.135 AC: 20533 AN: 152068 Hom.: 1483 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.135 AC: 20541 AN: 152186 Hom.: 1481 Cov.: 32 AF XY: 0.136 AC XY: 10133 AN XY: 74404

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.144

Alfa AF: 0.130 Hom.: 1803

Bravo AF: 0.145

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11747728; hg19: chr5-174863502;