15-47783356-A-G

Variant names:

• chr15-47783356-A-G
• rs607289
• ENST00000558792.6:n.572-8948T>C

Variant summary

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

The ENST00000558792.6(LINC01491):​n.572-8948T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,118 control chromosomes in the GnomAD database, including 30,684 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 (30684 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558792.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558792.6	TSL:3	n.572-8948T>C		intron	N/A
	LINC01491	ENST00000651940.1		n.579+7751T>C		intron	N/A
	LINC01491	ENST00000653152.1		n.619+7751T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96062 AN: 152000 Hom.: 30658 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.632 AC: 96128 AN: 152118 Hom.: 30684 Cov.: 33 AF XY: 0.642 AC XY: 47717 AN XY: 74346

African (AFR) AF: 0.601 AC: 24937 AN: 41484

American (AMR) AF: 0.655 AC: 10022 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2230 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3936 AN: 5168

South Asian (SAS) AF: 0.633 AC: 3059 AN: 4832

European-Finnish (FIN) AF: 0.750 AC: 7933 AN: 10576

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

European-Non Finnish (NFE) AF: 0.618 AC: 42021 AN: 67978

Other (OTH) AF: 0.637 AC: 1343 AN: 2108

Alfa AF: 0.606 Hom.: 10538

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.010
DANN	Benign	0.26
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs607289; hg19: chr15-48075553;