rs596942

Positions:

• chr15-47789954-C-T

Variant summary

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

The ENST00000653152.1(LINC01491):​n.619+1153G>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 0.0901 in 152,126 control chromosomes in the GnomAD database, including 965 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 0.090 (965 hom., cov: 33)
• Consequence: LINC01491 ENST00000653152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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
LINC01491	ENST00000653152.1	n.619+1153G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13699 AN: 152008 Hom.: 965 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0901 AC: 13712 AN: 152126 Hom.: 965 Cov.: 33 AF XY: 0.0955 AC XY: 7101 AN XY: 74366

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0716 Hom.: 165

Bravo AF: 0.0987

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs596942; hg19: chr15-48082151;