11-127574370-C-T

Variant names:

• chr11-127574370-C-T
• rs356258

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 0.781 in 152,064 control chromosomes in the GnomAD database, including 47,274 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 0.78 (47274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.781 AC: 118643 AN: 151946 Hom.: 47222 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.781 AC: 118758 AN: 152064 Hom.: 47274 Cov.: 31 AF XY: 0.784 AC XY: 58246 AN XY: 74304

African (AFR) AF: 0.934 AC: 38772 AN: 41520

American (AMR) AF: 0.774 AC: 11832 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3470

East Asian (EAS) AF: 0.931 AC: 4810 AN: 5164

South Asian (SAS) AF: 0.713 AC: 3424 AN: 4802

European-Finnish (FIN) AF: 0.725 AC: 7656 AN: 10560

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47115 AN: 67946

Other (OTH) AF: 0.772 AC: 1629 AN: 2110

Alfa AF: 0.724 Hom.: 52983

Bravo AF: 0.795

Asia WGS AF: 0.807 AC: 2806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.65
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs356258; hg19: chr11-127444265;