11-93076039-G-T

Variant names:

• chr11-93076039-G-T
• rs1876602

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 0.424 in 150,788 control chromosomes in the GnomAD database, including 14,417 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 0.42 (14417 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.424 AC: 63849 AN: 150662 Hom.: 14412 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.424 AC: 63879 AN: 150788 Hom.: 14417 Cov.: 33 AF XY: 0.430 AC XY: 31699 AN XY: 73700

African (AFR) AF: 0.257 AC: 10527 AN: 40976

American (AMR) AF: 0.529 AC: 8038 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1455 AN: 3460

East Asian (EAS) AF: 0.575 AC: 2879 AN: 5006

South Asian (SAS) AF: 0.468 AC: 2150 AN: 4592

European-Finnish (FIN) AF: 0.534 AC: 5596 AN: 10484

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31472 AN: 67770

Other (OTH) AF: 0.424 AC: 891 AN: 2102

Alfa AF: 0.427 Hom.: 7782

Bravo AF: 0.413

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.72
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs1876602; hg19: chr11-92809205;