rs11042937

Variant names:

• chr11-10723847-G-T
• rs11042937

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;