rs11042937

chr11-10723847-G-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 0.589 in 152,116 control chromosomes in the GnomAD database, including 27,403 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 0.59 (27403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.588 AC: 89438 AN: 151998 Hom.: 27352 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.589 AC: 89546 AN: 152116 Hom.: 27403 Cov.: 33 AF XY: 0.588 AC XY: 43746 AN XY: 74356

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.591

Alfa AF: 0.523 Hom.: 40528

Bravo AF: 0.617

Asia WGS AF: 0.667 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.037
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11042937; hg19: chr11-10745394;