ENST00000581648.2:n.1311-8724G>A

Variant names:

• chr18-24526812-C-T
• rs7235440
• ENST00000581648.2:n.1311-8724G>A

Variant summary

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

The ENST00000581648.2(ENSG00000266489):​n.1311-8724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,698 control chromosomes in the GnomAD database, including 16,788 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 0.46 (16788 hom., cov: 31)
• Consequence: ENSG00000266489 ENST00000581648.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 7 publications found

Genes affected

ENSG00000266489 (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 (AFR) allele frequency at 95% confidence interval = 0.586 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
ENSG00000266489	ENST00000581648.2	n.1311-8724G>A		intron_variant	Intron 1 of 2	3
ENSG00000266489	ENST00000662616.1	n.367-5441G>A		intron_variant	Intron 1 of 1
ENSG00000266489	ENST00000668994.2	n.357-8724G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69566 AN: 151580 Hom.: 16768 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.459 AC: 69633 AN: 151698 Hom.: 16788 Cov.: 31 AF XY: 0.460 AC XY: 34071 AN XY: 74108

African (AFR) AF: 0.592 AC: 24480 AN: 41346

American (AMR) AF: 0.504 AC: 7677 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1409 AN: 3466

East Asian (EAS) AF: 0.583 AC: 3004 AN: 5156

South Asian (SAS) AF: 0.469 AC: 2243 AN: 4780

European-Finnish (FIN) AF: 0.365 AC: 3831 AN: 10502

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25370 AN: 67894

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.409 Hom.: 43214

Bravo AF: 0.476

Asia WGS AF: 0.552 AC: 1917 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	2.0
DANN	Benign	0.16
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7235440; hg19: chr18-22106776;