rs10513909

Variant names:

• chr18-22492608-G-A
• rs10513909
• ENST00000731115.1:n.258-16242C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-22492608-G-A
• chr18-22492608-G-C

Variant summary

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

The ENST00000731115.1(ENSG00000289624):​n.258-16242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,772 control chromosomes in the GnomAD database, including 3,047 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 0.17 (3047 hom., cov: 31)
• Consequence: ENSG00000289624 ENST00000731115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 3 publications found

Genes affected

ENSG00000289624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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
ENSG00000289624	ENST00000731115.1	n.258-16242C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25901 AN: 151654 Hom.: 3037 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0976

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.171 AC: 25948 AN: 151772 Hom.: 3047 Cov.: 31 AF XY: 0.171 AC XY: 12670 AN XY: 74144

African (AFR) AF: 0.339 AC: 14021 AN: 41322

American (AMR) AF: 0.113 AC: 1724 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3466

East Asian (EAS) AF: 0.0974 AC: 500 AN: 5134

South Asian (SAS) AF: 0.151 AC: 724 AN: 4806

European-Finnish (FIN) AF: 0.122 AC: 1287 AN: 10508

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6844 AN: 67974

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.115 Hom.: 1529

Bravo AF: 0.177

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs10513909; hg19: chr18-20072571;