rs11038830

Positions:

• chr11-46240471-T-C

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 0.139 in 152,212 control chromosomes in the GnomAD database, including 1,663 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 0.14 (1663 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.140 AC: 21225 AN: 152094 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 21232 AN: 152212 Hom.: 1663 Cov.: 32 AF XY: 0.137 AC XY: 10171 AN XY: 74446

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.145

Alfa AF: 0.127 Hom.: 1304

Bravo AF: 0.142

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11038830; hg19: chr11-46262022;