15-47824200-T-C

Variant summary

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

The NR_120336.1(LINC01491):n.282+3371A>G 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 0.485 in 152,094 control chromosomes in the GnomAD database, including 21,976 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 0.49 (21976 hom., cov: 33)
• Consequence: LINC01491 NR_120336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01491	NR_120336.1	n.282+3371A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.318+3359A>G		intron_variant, non_coding_transcript_variant
	ENST00000662551.1	n.188+11284T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73719 AN: 151976 Hom.: 21921 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.485 AC: 73837 AN: 152094 Hom.: 21976 Cov.: 33 AF XY: 0.486 AC XY: 36162 AN XY: 74350

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.450

Alfa AF: 0.289 Hom.: 1681

Bravo AF: 0.513

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.7
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs494230; hg19: chr15-48116397;