11-127574370-C-T

Position:

• chr11-127574370-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.772

Alfa AF: 0.714 Hom.: 39579

Bravo AF: 0.795

Asia WGS AF: 0.807 AC: 2806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs356258; hg19: chr11-127444265;