rs10502525

Variant names:

• chr18-29085706-G-A
• rs10502525
• ENST00000789716.1:n.273-264C>T

Variant summary

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

The ENST00000789716.1(ENSG00000302813):​n.273-264C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,942 control chromosomes in the GnomAD database, including 46,970 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 0.78 (46970 hom., cov: 32)
• Consequence: ENSG00000302813 ENST00000789716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 3 publications found

Genes affected

ENSG00000302813 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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
ENSG00000302813	ENST00000789716.1	n.273-264C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118836 AN: 151824 Hom.: 46940 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.783 AC: 118920 AN: 151942 Hom.: 46970 Cov.: 32 AF XY: 0.783 AC XY: 58125 AN XY: 74242

African (AFR) AF: 0.669 AC: 27717 AN: 41418

American (AMR) AF: 0.851 AC: 12975 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3074 AN: 3460

East Asian (EAS) AF: 0.973 AC: 4992 AN: 5128

South Asian (SAS) AF: 0.786 AC: 3783 AN: 4810

European-Finnish (FIN) AF: 0.769 AC: 8137 AN: 10580

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55573 AN: 67986

Other (OTH) AF: 0.826 AC: 1744 AN: 2112

Alfa AF: 0.805 Hom.: 26409

Bravo AF: 0.790

Asia WGS AF: 0.870 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.80
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10502525; hg19: chr18-26665670;