rs616614

Variant names:

• chr15-47809813-T-C
• rs616614
• ENST00000558792.6:n.414+4258A>G

Variant summary

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

The ENST00000558792.6(LINC01491):​n.414+4258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,106 control chromosomes in the GnomAD database, including 35,490 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 0.67 (35490 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 3 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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
	LINC01491	NR_120336.1		n.283-4935A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558792.6	TSL:3	n.414+4258A>G		intron	N/A
	LINC01491	ENST00000651940.1		n.278+4258A>G		intron	N/A
	LINC01491	ENST00000653152.1		n.319-4935A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101040 AN: 151988 Hom.: 35432 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.665 AC: 101162 AN: 152106 Hom.: 35490 Cov.: 32 AF XY: 0.666 AC XY: 49482 AN XY: 74350

African (AFR) AF: 0.901 AC: 37410 AN: 41530

American (AMR) AF: 0.646 AC: 9863 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3851 AN: 5164

South Asian (SAS) AF: 0.683 AC: 3298 AN: 4826

European-Finnish (FIN) AF: 0.514 AC: 5422 AN: 10558

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37082 AN: 67974

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.604 Hom.: 24790

Bravo AF: 0.685

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs616614;

hg19: chr15-48102010;