rs11038830

Variant names:

• chr11-46240471-T-C
• rs11038830

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;