15-47843367-C-T

Position:

• chr15-47843367-C-T

Variant summary

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

The NR_120336.1(LINC01491):​n.236+1471G>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 0.519 in 152,022 control chromosomes in the GnomAD database, including 21,458 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 0.52 (21458 hom., cov: 33)
• Consequence: LINC01491 NR_120336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.236+1471G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000653152.1	n.260+1471G>A		intron_variant, non_coding_transcript_variant
	ENST00000662551.1	n.188+30451C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78793 AN: 151902 Hom.: 21416 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.519 AC: 78892 AN: 152022 Hom.: 21458 Cov.: 33 AF XY: 0.523 AC XY: 38863 AN XY: 74274

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.522

Alfa AF: 0.465 Hom.: 13115

Bravo AF: 0.532

Asia WGS AF: 0.681 AC: 2367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs785016; hg19: chr15-48135564;