11-2127541-G-T

Variant names:

• chr11-2127541-G-T
• rs4261263

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 0.596 in 151,402 control chromosomes in the GnomAD database, including 27,169 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 0.60 (27169 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90128 AN: 151282 Hom.: 27140 Cov.: 30

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.596 AC: 90215 AN: 151402 Hom.: 27169 Cov.: 30 AF XY: 0.595 AC XY: 43984 AN XY: 73940

African (AFR) AF: 0.526 AC: 21678 AN: 41196

American (AMR) AF: 0.685 AC: 10442 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2077 AN: 3462

East Asian (EAS) AF: 0.483 AC: 2467 AN: 5110

South Asian (SAS) AF: 0.469 AC: 2255 AN: 4810

European-Finnish (FIN) AF: 0.649 AC: 6817 AN: 10500

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42399 AN: 67766

Other (OTH) AF: 0.581 AC: 1225 AN: 2108

Alfa AF: 0.612 Hom.: 6322

Bravo AF: 0.597

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.85
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4261263; hg19: chr11-2148771;