rs10519150

Variant names:

• chr15-47846958-G-A
• rs10519150
• ENST00000662551.1:n.188+34042G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-47846958-G-A
• chr15-47846958-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662551.1(ENSG00000259754):​n.188+34042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,060 control chromosomes in the GnomAD database, including 948 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 0.094 (948 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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
ENSG00000259754	ENST00000662551.1	n.188+34042G>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+34042G>A		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+34042G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14245 AN: 151942 Hom.: 950 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0937 AC: 14249 AN: 152060 Hom.: 948 Cov.: 32 AF XY: 0.0963 AC XY: 7153 AN XY: 74312

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0815 Hom.: 1327

Bravo AF: 0.0928

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519150; hg19: chr15-48139155; COSMIC: COSV73633910;