chr15-47846958-G-A

Variant names:

• chr15-47846958-G-A
• rs10519150
• ENST00000789565.1:n.963G>A

Variant summary

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

The ENST00000789565.1(ENSG00000259754):​n.963G>A variant causes a non coding transcript exon 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 ENST00000789565.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 1 publications found

Genes affected

ENSG00000259754 (HGNC:):

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000789565.1	n.963G>A		non_coding_transcript_exon_variant	Exon 4 of 4
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

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

African (AFR) AF: 0.0490 AC: 2033 AN: 41508

American (AMR) AF: 0.132 AC: 2011 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1658 AN: 5154

South Asian (SAS) AF: 0.129 AC: 621 AN: 4812

European-Finnish (FIN) AF: 0.150 AC: 1579 AN: 10560

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0870 AC: 5911 AN: 67970

Other (OTH) AF: 0.0859 AC: 181 AN: 2108

Alfa AF: 0.0833 Hom.: 2174

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
PhyloP100		1.6

Splicing

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

Other links and lift over

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