rs11035042

chr11-4993704-A-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 0.0801 in 152,202 control chromosomes in the GnomAD database, including 626 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 0.080 (626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

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 = 0.164 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: 0.0801 AC: 12180 AN: 152082 Hom.: 622 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0801 AC: 12196 AN: 152202 Hom.: 626 Cov.: 32 AF XY: 0.0829 AC XY: 6170 AN XY: 74418

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0927 Hom.: 91

Bravo AF: 0.0739

Asia WGS AF: 0.103 AC: 358 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.3
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11035042; hg19: chr11-5014934;