rs10513910

Variant names:

• chr18-22492467-G-A
• rs10513910
• ENST00000731115.1:n.258-16101C>T

Variant summary

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

The ENST00000731115.1(ENSG00000289624):​n.258-16101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 152,116 control chromosomes in the GnomAD database, including 1,099 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 0.097 (1099 hom., cov: 32)
• Consequence: ENSG00000289624 ENST00000731115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731115.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289624	ENST00000731115.1		n.258-16101C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14707 AN: 151998 Hom.: 1096 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0968 AC: 14721 AN: 152116 Hom.: 1099 Cov.: 32 AF XY: 0.0958 AC XY: 7126 AN XY: 74370

African (AFR) AF: 0.208 AC: 8636 AN: 41448

American (AMR) AF: 0.0642 AC: 981 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.0970 AC: 501 AN: 5166

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4818

European-Finnish (FIN) AF: 0.0530 AC: 562 AN: 10598

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0468 AC: 3182 AN: 68012

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0805 Hom.: 94

Bravo AF: 0.103

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.50
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10513910; hg19: chr18-20072430;