rs10512152

Variant names:

• chr9-84612894-A-G
• rs10512152
• ENST00000650453.1:n.1341+897A>G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.1341+897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,264 control chromosomes in the GnomAD database, including 78 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 0.026 (78 hom., cov: 33)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 4 publications found

Genes affected

ENSG00000285987 (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 (AMR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. 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
	ENSG00000285987	ENST00000650453.1		n.1341+897A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0262 AC: 3987 AN: 152146 Hom.: 78 Cov.: 33

Gnomad AFR AF: 0.00731

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0262 AC: 3987 AN: 152264 Hom.: 78 Cov.: 33 AF XY: 0.0266 AC XY: 1982 AN XY: 74452

African (AFR) AF: 0.00729 AC: 303 AN: 41570

American (AMR) AF: 0.0545 AC: 833 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3472

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5186

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4832

European-Finnish (FIN) AF: 0.0294 AC: 311 AN: 10592

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1990 AN: 68004

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0303 Hom.: 65

Bravo AF: 0.0283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.80
PhyloP100		-2.1

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: rs10512152;

hg19: chr9-87227809;