15-47818455-A-T

Position:

• chr15-47818455-A-T

Variant summary

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

The NR_120336.1(LINC01491):​n.282+9116T>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 0.342 in 152,000 control chromosomes in the GnomAD database, including 10,776 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 0.34 (10776 hom., cov: 32)
• Consequence: LINC01491 NR_120336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01491	NR_120336.1	n.282+9116T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.318+9104T>A		intron_variant, non_coding_transcript_variant
	ENST00000662551.1	n.188+5539A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52001 AN: 151882 Hom.: 10774 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.342 AC: 52015 AN: 152000 Hom.: 10776 Cov.: 32 AF XY: 0.342 AC XY: 25412 AN XY: 74302

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.353

Alfa AF: 0.396 Hom.: 1639

Bravo AF: 0.323

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1669832; hg19: chr15-48110652;