rs16960139

chr15-47792483-G-A

Variant summary

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

The ENST00000653152.1(LINC01491):n.476-1233C>T 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 0.0273 in 152,286 control chromosomes in the GnomAD database, including 229 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 0.027 (229 hom., cov: 33)
• Consequence: LINC01491 ENST00000653152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 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.476-1233C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4150 AN: 152168 Hom.: 231 Cov.: 33

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00700

Gnomad OTH AF: 0.0312

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

GnomAD4 genome AF: 0.0273 AC: 4155 AN: 152286 Hom.: 229 Cov.: 33 AF XY: 0.0287 AC XY: 2139 AN XY: 74480

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00698

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0117 Hom.: 9

Bravo AF: 0.0331

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.068
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960139; hg19: chr15-48084680;