rs11634357

chr15-81697597-G-Achr15-81697597-G-T

Variant summary

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

The ENST00000559211.1(ENSG00000259543):n.267-55983G>A variant causes a intron, non coding transcript 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: ENST00000559211.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559211.1	n.267-55983G>A		intron_variant, non_coding_transcript_variant		4
LINC01418	ENST00000559428.2	n.96-55162C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.250

Alfa AF: 0.133 Hom.: 232

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

Splicing

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

Publications

LitVar

Other links and lift over

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