rs647903

Variant names:

• chr15-47798219-G-C
• rs647903
• ENST00000558792.6:n.571+5165C>G

Variant summary

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

The ENST00000558792.6(LINC01491):​n.571+5165C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,006 control chromosomes in the GnomAD database, including 23,195 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 0.54 (23195 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• 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=-1.11).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558792.6	TSL:3	n.571+5165C>G		intron	N/A
	LINC01491	ENST00000651940.1		n.435+5165C>G		intron	N/A
	LINC01491	ENST00000653152.1		n.475+5165C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82373 AN: 151888 Hom.: 23154 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82481 AN: 152006 Hom.: 23195 Cov.: 32 AF XY: 0.550 AC XY: 40854 AN XY: 74302

African (AFR) AF: 0.638 AC: 26468 AN: 41454

American (AMR) AF: 0.589 AC: 8988 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.872 AC: 4513 AN: 5174

South Asian (SAS) AF: 0.599 AC: 2880 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 5015 AN: 10558

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30970 AN: 67968

Other (OTH) AF: 0.573 AC: 1210 AN: 2110

Alfa AF: 0.493 Hom.: 2347

Bravo AF: 0.555

Asia WGS AF: 0.726 AC: 2517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.36
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs647903; hg19: chr15-48090416;