rs10512019

Variant names:

• chr9-73336360-T-C
• rs10512019
• ENST00000715867.1:n.95-22448T>C

Variant summary

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

The ENST00000715867.1(ENSG00000293608):​n.95-22448T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,248 control chromosomes in the GnomAD database, including 87 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 0.027 (87 hom., cov: 32)
• Consequence: ENSG00000293608 ENST00000715867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0633 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.95-22448T>C		intron	N/A
	ENSG00000293608	ENST00000715868.1		n.101-22448T>C		intron	N/A
	ENSG00000293608	ENST00000715869.1		n.83-75225T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4111 AN: 152130 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0270 AC: 4110 AN: 152248 Hom.: 87 Cov.: 32 AF XY: 0.0266 AC XY: 1978 AN XY: 74452

African (AFR) AF: 0.0654 AC: 2716 AN: 41536

American (AMR) AF: 0.0192 AC: 293 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3472

East Asian (EAS) AF: 0.0255 AC: 132 AN: 5176

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4824

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10620

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 695 AN: 68018

Other (OTH) AF: 0.0232 AC: 49 AN: 2110

Alfa AF: 0.0146 Hom.: 10

Bravo AF: 0.0288

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.23

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: rs10512019;

hg19: chr9-75951276;