rs11127958

Variant names:

• chr3-86776450-A-T
• rs11127958
• ENST00000760372.1:n.236-23042A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000760372.1(ENSG00000299083):​n.236-23042A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,934 control chromosomes in the GnomAD database, including 8,505 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 0.33 (8505 hom., cov: 32)
• Consequence: ENSG00000299083 ENST00000760372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 5 publications found

Genes affected

ENSG00000299083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 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
ENSG00000299083	ENST00000760372.1	n.236-23042A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50462 AN: 151814 Hom.: 8497 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.332 AC: 50488 AN: 151934 Hom.: 8505 Cov.: 32 AF XY: 0.330 AC XY: 24518 AN XY: 74260

African (AFR) AF: 0.302 AC: 12515 AN: 41432

American (AMR) AF: 0.320 AC: 4884 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 940 AN: 3460

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5174

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4812

European-Finnish (FIN) AF: 0.334 AC: 3526 AN: 10558

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24904 AN: 67922

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.361 Hom.: 1228

Bravo AF: 0.328

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.51
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs11127958; hg19: chr3-86825600; COSMIC: COSV70613037;