rs10518945

Variant names:

• chr15-57894770-A-G
• rs10518945
• ENST00000728742.1:n.*53A>G

Variant summary

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

The ENST00000728742.1(ENSG00000295231):​n.*53A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,202 control chromosomes in the GnomAD database, including 5,921 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 0.28 (5921 hom., cov: 32)
• Consequence: ENSG00000295231 ENST00000728742.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 2 publications found

Genes affected

ENSG00000295231 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295231	ENST00000728742.1	n.*53A>G		downstream_gene_variant
ENSG00000295231	ENST00000728743.1	n.*59A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 42002 AN: 152084 Hom.: 5916 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.276 AC: 42035 AN: 152202 Hom.: 5921 Cov.: 32 AF XY: 0.279 AC XY: 20732 AN XY: 74420

African (AFR) AF: 0.337 AC: 13991 AN: 41506

American (AMR) AF: 0.258 AC: 3946 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1788 AN: 5184

South Asian (SAS) AF: 0.334 AC: 1611 AN: 4824

European-Finnish (FIN) AF: 0.272 AC: 2878 AN: 10596

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15940 AN: 68006

Other (OTH) AF: 0.278 AC: 588 AN: 2116

Alfa AF: 0.250 Hom.: 3108

Bravo AF: 0.273

Asia WGS AF: 0.327 AC: 1136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10518945; hg19: chr15-58186968;