11-56672760-C-T

Variant names:

• chr11-56672760-C-T
• rs11228719
• ENST00000641232.1:n.180-1340G>A

Variant summary

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

The ENST00000641232.1(ENSG00000290752):​n.180-1340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 143,990 control chromosomes in the GnomAD database, including 28,749 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 (28749 hom., cov: 30)
• Consequence: ENSG00000290752 ENST00000641232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 6 publications found

Genes affected

ENSG00000290752 (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 = 0.759 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
ENSG00000290752	ENST00000641232.1	n.180-1340G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 86929 AN: 143864 Hom.: 28734 Cov.: 30

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.604 AC: 86964 AN: 143990 Hom.: 28749 Cov.: 30 AF XY: 0.609 AC XY: 42761 AN XY: 70242

African (AFR) AF: 0.353 AC: 14357 AN: 40668

American (AMR) AF: 0.731 AC: 10624 AN: 14524

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2187 AN: 3398

East Asian (EAS) AF: 0.779 AC: 3990 AN: 5122

South Asian (SAS) AF: 0.747 AC: 3436 AN: 4598

European-Finnish (FIN) AF: 0.708 AC: 6596 AN: 9310

Middle Eastern (MID) AF: 0.629 AC: 176 AN: 280

European-Non Finnish (NFE) AF: 0.691 AC: 43703 AN: 63254

Other (OTH) AF: 0.643 AC: 1259 AN: 1958

Alfa AF: 0.643 Hom.: 46149

Asia WGS AF: 0.725 AC: 2513 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.36
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11228719; hg19: chr11-56440236;