chr11-124049938-G-C

Variant names:

• chr11-124049938-G-C
• rs4936891

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 0.587 in 151,738 control chromosomes in the GnomAD database, including 28,282 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 0.59 (28282 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.587 AC: 88987 AN: 151618 Hom.: 28210 Cov.: 30

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.587 AC: 89126 AN: 151738 Hom.: 28282 Cov.: 30 AF XY: 0.596 AC XY: 44167 AN XY: 74150

African (AFR) AF: 0.819 AC: 33883 AN: 41348

American (AMR) AF: 0.598 AC: 9127 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1754 AN: 3468

East Asian (EAS) AF: 0.778 AC: 4006 AN: 5146

South Asian (SAS) AF: 0.641 AC: 3084 AN: 4810

European-Finnish (FIN) AF: 0.516 AC: 5414 AN: 10498

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.445 AC: 30223 AN: 67908

Other (OTH) AF: 0.539 AC: 1132 AN: 2100

Alfa AF: 0.340 Hom.: 803

Bravo AF: 0.599

Asia WGS AF: 0.752 AC: 2612 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	0.32
DANN	Benign	0.44
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4936891; hg19: chr11-123920645;