rs11167102

Variant names:

• chr8-141890509-G-A
• rs11167102

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 0.517 in 152,044 control chromosomes in the GnomAD database, including 20,409 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 0.52 (20409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78536 AN: 151924 Hom.: 20393 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.517 AC: 78592 AN: 152044 Hom.: 20409 Cov.: 32 AF XY: 0.517 AC XY: 38432 AN XY: 74308

African (AFR) AF: 0.483 AC: 20041 AN: 41454

American (AMR) AF: 0.581 AC: 8882 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5150

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4810

European-Finnish (FIN) AF: 0.525 AC: 5557 AN: 10586

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35934 AN: 67968

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.521 Hom.: 4111

Bravo AF: 0.521

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.23
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11167102; hg19: chr8-142971870;