rs616614

chr15-47809813-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.283-4935A>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 0.665 in 152,106 control chromosomes in the GnomAD database, including 35,490 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 0.67 (35490 hom., cov: 32)
• Consequence: LINC01491 NR_120336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01491	NR_120336.1	n.283-4935A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.319-4935A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101040 AN: 151988 Hom.: 35432 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.665 AC: 101162 AN: 152106 Hom.: 35490 Cov.: 32 AF XY: 0.666 AC XY: 49482 AN XY: 74350

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.670

Alfa AF: 0.587 Hom.: 16515

Bravo AF: 0.685

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.15
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs616614; hg19: chr15-48102010;