rs634939

Variant names:

• chr15-47778580-C-T
• rs634939
• ENST00000558792.6:n.572-4172G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558792.6(LINC01491):​n.572-4172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,922 control chromosomes in the GnomAD database, including 30,469 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 0.63 (30469 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.572-4172G>A		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.580-4172G>A		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.620-4172G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95681 AN: 151804 Hom.: 30442 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.630 AC: 95742 AN: 151922 Hom.: 30469 Cov.: 33 AF XY: 0.640 AC XY: 47544 AN XY: 74234

African (AFR) AF: 0.596 AC: 24695 AN: 41408

American (AMR) AF: 0.654 AC: 9988 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2227 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3935 AN: 5182

South Asian (SAS) AF: 0.633 AC: 3047 AN: 4814

European-Finnish (FIN) AF: 0.749 AC: 7904 AN: 10548

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41955 AN: 67906

Other (OTH) AF: 0.636 AC: 1346 AN: 2116

Alfa AF: 0.636 Hom.: 3835

Bravo AF: 0.623

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs634939; hg19: chr15-48070777; COSMIC: COSV60373612;