rs2234689

Variant names:

• chr11-113407761-G-C
• rs2234689
• ENST00000546284.1:n.244+1794G>C

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.244+1794G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,234 control chromosomes in the GnomAD database, including 51,769 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 0.82 (51769 hom., cov: 34)
• Consequence: ENSG00000256757 ENST00000546284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 23 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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+1794G>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125350 AN: 152116 Hom.: 51730 Cov.: 34

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.824 AC: 125442 AN: 152234 Hom.: 51769 Cov.: 34 AF XY: 0.827 AC XY: 61564 AN XY: 74432

African (AFR) AF: 0.811 AC: 33675 AN: 41518

American (AMR) AF: 0.844 AC: 12904 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3468

East Asian (EAS) AF: 0.961 AC: 4966 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4043 AN: 4824

European-Finnish (FIN) AF: 0.858 AC: 9114 AN: 10618

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55281 AN: 68018

Other (OTH) AF: 0.826 AC: 1746 AN: 2114

Alfa AF: 0.823 Hom.: 6416

Bravo AF: 0.825

Asia WGS AF: 0.861 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.42
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2234689; hg19: chr11-113278483;