rs649530

Variant names:

• chr18-2172132-G-A
• rs649530
• ENST00000579097.1:n.89-40592C>T

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.89-40592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,724 control chromosomes in the GnomAD database, including 21,563 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 0.52 (21563 hom., cov: 30)
• Consequence: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 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
ENSG00000263745	ENST00000579097.1	n.89-40592C>T		intron_variant	Intron 1 of 3	2
ENSG00000263745	ENST00000584867.1	n.196+67661C>T		intron_variant	Intron 2 of 5	2
ENSG00000263745	ENST00000639316.2	n.442-45755C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79439 AN: 151606 Hom.: 21546 Cov.: 30

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.524 AC: 79483 AN: 151724 Hom.: 21563 Cov.: 30 AF XY: 0.530 AC XY: 39339 AN XY: 74168

African (AFR) AF: 0.375 AC: 15500 AN: 41310

American (AMR) AF: 0.558 AC: 8509 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2664 AN: 5140

South Asian (SAS) AF: 0.604 AC: 2903 AN: 4808

European-Finnish (FIN) AF: 0.700 AC: 7362 AN: 10522

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

European-Non Finnish (NFE) AF: 0.573 AC: 38933 AN: 67910

Other (OTH) AF: 0.531 AC: 1119 AN: 2108

Alfa AF: 0.541 Hom.: 7567

Bravo AF: 0.503

Asia WGS AF: 0.539 AC: 1876 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs649530; hg19: chr18-2172132;