rs10512017

Variant names:

• chr9-73269323-G-A
• rs10512017
• ENST00000715867.1:n.94+64192G>A

Variant summary

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

The ENST00000715867.1(ENSG00000293608):​n.94+64192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 152,220 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: -0.738
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293608	ENST00000715867.1		n.94+64192G>A		intron	N/A
	ENSG00000293608	ENST00000715868.1		n.100+9966G>A		intron	N/A
	ENSG00000293608	ENST00000715869.1		n.82+9966G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3828 AN: 152102 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00659

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0251 AC: 3827 AN: 152220 Hom.: 85 Cov.: 32 AF XY: 0.0248 AC XY: 1848 AN XY: 74434

African (AFR) AF: 0.0652 AC: 2709 AN: 41524

American (AMR) AF: 0.0189 AC: 289 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3462

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5180

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4826

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: 68012

Other (OTH) AF: 0.0189 AC: 40 AN: 2114

Alfa AF: 0.0151 Hom.: 20

Bravo AF: 0.0277

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.71
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10512017;

hg19: chr9-75884239;