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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724036	XR_001746805.1	n.158-2898A>C		intron_variant	Intron 2 of 13
LOC102724036	XR_007061622.1	n.158-2898A>C		intron_variant	Intron 2 of 16
LOC102724036	XR_007061623.1	n.158-2898A>C		intron_variant	Intron 2 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.537-2898A>C		intron_variant	Intron 1 of 6
ENSG00000285987	ENST00000728338.1	n.462-2898A>C		intron_variant	Intron 2 of 6
ENSG00000285987	ENST00000728339.1	n.342-2898A>C		intron_variant	Intron 1 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs10512148; hg19: chr9-87109486;