rs11035042

Variant names:

• chr11-4993704-A-T
• rs11035042

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0185 AC: 770 AN: 41576

American (AMR) AF: 0.0706 AC: 1079 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.173 AC: 899 AN: 5184

South Asian (SAS) AF: 0.0761 AC: 368 AN: 4834

European-Finnish (FIN) AF: 0.142 AC: 1506 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7159 AN: 67954

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.3
DANN	Benign	0.42
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs11035042; hg19: chr11-5014934;