11-92986041-T-G

Variant names:

• chr11-92986041-T-G
• rs4611171

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 0.558 in 152,016 control chromosomes in the GnomAD database, including 24,000 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 0.56 (24000 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.558 AC: 84703 AN: 151900 Hom.: 23968 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.558 AC: 84797 AN: 152016 Hom.: 24000 Cov.: 33 AF XY: 0.566 AC XY: 42053 AN XY: 74310

African (AFR) AF: 0.560 AC: 23204 AN: 41468

American (AMR) AF: 0.658 AC: 10050 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3591 AN: 5156

South Asian (SAS) AF: 0.687 AC: 3309 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6074 AN: 10558

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

European-Non Finnish (NFE) AF: 0.517 AC: 35106 AN: 67948

Other (OTH) AF: 0.543 AC: 1148 AN: 2114

Alfa AF: 0.556 Hom.: 4043

Bravo AF: 0.565

Asia WGS AF: 0.650 AC: 2258 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	1.4
DANN	Benign	0.62
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4611171; hg19: chr11-92719207;