15-81697597-G-A

Variant names:

• chr15-81697597-G-A
• rs11634357
• ENST00000829426.1:n.67C>T

Variant summary

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

The ENST00000829426.1(LINC01418):​n.67C>T 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 0.246 in 152,012 control chromosomes in the GnomAD database, including 5,790 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 0.25 (5790 hom., cov: 32)
• Consequence: LINC01418 ENST00000829426.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

Genes affected

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ENSG00000259543 (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 (NFE) allele frequency at 95% confidence interval = 0.345 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
LINC01418	ENST00000829426.1	n.67C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000259543	ENST00000559211.1	n.267-55983G>A		intron_variant	Intron 2 of 3	4
LINC01418	ENST00000559428.2	n.96-55162C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37342 AN: 151894 Hom.: 5789 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.246 AC: 37337 AN: 152012 Hom.: 5790 Cov.: 32 AF XY: 0.244 AC XY: 18147 AN XY: 74304

African (AFR) AF: 0.0725 AC: 3011 AN: 41556

American (AMR) AF: 0.237 AC: 3622 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3468

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4812

European-Finnish (FIN) AF: 0.372 AC: 3934 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23632 AN: 67834

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.130 Hom.: 234

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs11634357; hg19: chr15-81989938; COSMIC: COSV73621952;