ENST00000583163.2:n.335+28496G>A

Variant names:

• chr18-1595020-G-A
• rs8097348
• ENST00000583163.2:n.335+28496G>A

Variant summary

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

The ENST00000583163.2(ENSG00000266602):​n.335+28496G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,782 control chromosomes in the GnomAD database, including 39,956 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 0.71 (39956 hom., cov: 31)
• Consequence: ENSG00000266602 ENST00000583163.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 14 publications found

Genes affected

ENSG00000266602 (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 = 0.942 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
ENSG00000266602	ENST00000583163.2	n.335+28496G>A		intron_variant	Intron 3 of 4	2
ENSG00000266602	ENST00000652957.2	n.275+28496G>A		intron_variant	Intron 2 of 2
ENSG00000266602	ENST00000653006.1	n.311+28496G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108094 AN: 151666 Hom.: 39934 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.713 AC: 108155 AN: 151782 Hom.: 39956 Cov.: 31 AF XY: 0.723 AC XY: 53649 AN XY: 74174

African (AFR) AF: 0.503 AC: 20830 AN: 41426

American (AMR) AF: 0.746 AC: 11366 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2564 AN: 3466

East Asian (EAS) AF: 0.964 AC: 4978 AN: 5164

South Asian (SAS) AF: 0.880 AC: 4242 AN: 4822

European-Finnish (FIN) AF: 0.860 AC: 9089 AN: 10566

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52520 AN: 67798

Other (OTH) AF: 0.718 AC: 1513 AN: 2108

Alfa AF: 0.737 Hom.: 58482

Bravo AF: 0.693

Asia WGS AF: 0.878 AC: 3047 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.21
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs8097348; hg19: chr18-1595021;