rs10512148

Variant names:

• chr9-84494571-A-C
• rs10512148
• ENST00000650453.1:n.537-2898A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-84494571-A-C
• chr9-84494571-A-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.537-2898A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,264 control chromosomes in the GnomAD database, including 248 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 0.043 (248 hom., cov: 33)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0934 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.537-2898A>C		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.462-2898A>C		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.342-2898A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6590 AN: 152146 Hom.: 246 Cov.: 33

Gnomad AFR AF: 0.00982

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0433 AC: 6596 AN: 152264 Hom.: 248 Cov.: 33 AF XY: 0.0471 AC XY: 3505 AN XY: 74446

African (AFR) AF: 0.00979 AC: 407 AN: 41568

American (AMR) AF: 0.0910 AC: 1391 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5182

South Asian (SAS) AF: 0.0304 AC: 147 AN: 4830

European-Finnish (FIN) AF: 0.115 AC: 1212 AN: 10584

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0392 AC: 2664 AN: 68018

Other (OTH) AF: 0.0406 AC: 86 AN: 2116

Alfa AF: 0.0235 Hom.: 19

Bravo AF: 0.0427

Asia WGS AF: 0.0670 AC: 230 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.42
PhyloP100		0.49

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: rs10512148;

hg19: chr9-87109486;