rs2242592

Variant names:

• chr11-113408708-G-A
• rs2242592
• ENST00000546284.1:n.244+2741G>A

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.244+2741G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,916 control chromosomes in the GnomAD database, including 26,799 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 0.57 (26799 hom., cov: 31)
• Consequence: ENSG00000256757 ENST00000546284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 38 publications found

Genes affected

ENSG00000256757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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
ENSG00000256757	ENST00000546284.1	n.244+2741G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86699 AN: 151798 Hom.: 26799 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.571 AC: 86717 AN: 151916 Hom.: 26799 Cov.: 31 AF XY: 0.569 AC XY: 42270 AN XY: 74234

African (AFR) AF: 0.322 AC: 13357 AN: 41420

American (AMR) AF: 0.608 AC: 9278 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2268 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2352 AN: 5142

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4814

European-Finnish (FIN) AF: 0.658 AC: 6943 AN: 10550

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47504 AN: 67948

Other (OTH) AF: 0.616 AC: 1298 AN: 2106

Alfa AF: 0.669 Hom.: 58252

Bravo AF: 0.560

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	-0.96
CADD	Benign	0.36
DANN	Benign	0.32
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2242592; hg19: chr11-113279430;