rs10512018

Variant names:

• chr9-73279894-A-G
• rs10512018
• ENST00000715867.1:n.94+74763A>G

Variant summary

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

The ENST00000715867.1(ENSG00000293608):​n.94+74763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,156 control chromosomes in the GnomAD database, including 85 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 0.025 (85 hom., cov: 32)
• Consequence: ENSG00000293608 ENST00000715867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.87
• Publications: 0 publications found

Genes affected

ENSG00000293608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927281	XR_001746723.2	n.67+20537A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293608	ENST00000715867.1	n.94+74763A>G		intron_variant	Intron 1 of 7
ENSG00000293608	ENST00000715868.1	n.100+20537A>G		intron_variant	Intron 1 of 7
ENSG00000293608	ENST00000715869.1	n.82+20537A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3835 AN: 152038 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00659

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0252 AC: 3834 AN: 152156 Hom.: 85 Cov.: 32 AF XY: 0.0250 AC XY: 1859 AN XY: 74386

African (AFR) AF: 0.0654 AC: 2717 AN: 41526

American (AMR) AF: 0.0187 AC: 285 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3468

East Asian (EAS) AF: 0.0268 AC: 139 AN: 5182

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4828

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00659 AC: 448 AN: 67964

Other (OTH) AF: 0.0190 AC: 40 AN: 2110

Alfa AF: 0.0147 Hom.: 18

Bravo AF: 0.0277

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs10512018; hg19: chr9-75894810;