rs11742270

chr5-35881341-G-A

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 0.2 in 152,062 control chromosomes in the GnomAD database, including 3,731 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 0.20 (3731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.200 AC: 30398 AN: 151944 Hom.: 3733 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.200 AC: 30399 AN: 152062 Hom.: 3731 Cov.: 32 AF XY: 0.202 AC XY: 15043 AN XY: 74336

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.184

Alfa AF: 0.235 Hom.: 1146

Bravo AF: 0.182

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11742270; hg19: chr5-35881443;