rs2531866

Variant names:

• chr17-27816138-G-A
• rs2531866
• ENST00000582441.1:c.220-11797C>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-11797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,082 control chromosomes in the GnomAD database, including 25,014 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 0.56 (25014 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 7 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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
ENSG00000266202	ENST00000582441.1	c.220-11797C>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84549 AN: 151964 Hom.: 25009 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.556 AC: 84585 AN: 152082 Hom.: 25014 Cov.: 32 AF XY: 0.561 AC XY: 41693 AN XY: 74316

African (AFR) AF: 0.345 AC: 14303 AN: 41478

American (AMR) AF: 0.631 AC: 9628 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3855 AN: 5172

South Asian (SAS) AF: 0.698 AC: 3368 AN: 4826

European-Finnish (FIN) AF: 0.634 AC: 6691 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42756 AN: 67996

Other (OTH) AF: 0.579 AC: 1225 AN: 2114

Alfa AF: 0.569 Hom.: 3331

Bravo AF: 0.547

Asia WGS AF: 0.683 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2531866; hg19: chr17-26143164;