rs2136531

Variant names:

• chr11-109030078-C-T
• rs2136531
• ENST00000526041.2:n.283+7665G>A

Variant summary

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

The ENST00000526041.2(ENSG00000255528):​n.283+7665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,876 control chromosomes in the GnomAD database, including 4,949 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 0.25 (4949 hom., cov: 31)
• Consequence: ENSG00000255528 ENST00000526041.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 2 publications found

Genes affected

ENSG00000255528 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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
ENSG00000255528	ENST00000526041.2	n.283+7665G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37481 AN: 151758 Hom.: 4933 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.247 AC: 37530 AN: 151876 Hom.: 4949 Cov.: 31 AF XY: 0.254 AC XY: 18817 AN XY: 74200

African (AFR) AF: 0.283 AC: 11700 AN: 41394

American (AMR) AF: 0.253 AC: 3862 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 706 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2355 AN: 5140

South Asian (SAS) AF: 0.281 AC: 1347 AN: 4800

European-Finnish (FIN) AF: 0.253 AC: 2669 AN: 10540

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14078 AN: 67954

Other (OTH) AF: 0.260 AC: 550 AN: 2114

Alfa AF: 0.225 Hom.: 706

Bravo AF: 0.248

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.0
DANN	Benign	0.74
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs2136531; hg19: chr11-108900805;