11-127240288-C-T

Variant names:

• chr11-127240288-C-T
• rs2514895

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 0.314 in 151,998 control chromosomes in the GnomAD database, including 10,991 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 0.31 (10991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• 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 = 0.645 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: 0.313 AC: 47580 AN: 151882 Hom.: 10954 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.314 AC: 47669 AN: 151998 Hom.: 10991 Cov.: 32 AF XY: 0.308 AC XY: 22911 AN XY: 74316

African (AFR) AF: 0.652 AC: 26998 AN: 41424

American (AMR) AF: 0.213 AC: 3252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1530 AN: 5150

South Asian (SAS) AF: 0.256 AC: 1227 AN: 4802

European-Finnish (FIN) AF: 0.133 AC: 1414 AN: 10594

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11670 AN: 67968

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.242 Hom.: 9466

Bravo AF: 0.337

Asia WGS AF: 0.309 AC: 1077 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.49
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2514895; hg19: chr11-127110183;