ENST00000558792.6:n.415-42A>G

Variant names:

• chr15-47804920-T-C
• rs477077
• ENST00000558792.6:n.415-42A>G

Variant summary

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

The ENST00000558792.6(LINC01491):​n.415-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,076 control chromosomes in the GnomAD database, including 17,281 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 0.46 (17281 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 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
	LINC01491	NR_120336.1		n.283-42A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01491	ENST00000558792.6	TSL:3	n.415-42A>G		intron	N/A
	LINC01491	ENST00000651940.1		n.279-42A>G		intron	N/A
	LINC01491	ENST00000653152.1		n.319-42A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70116 AN: 151956 Hom.: 17247 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.447

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.462 AC: 70210 AN: 152076 Hom.: 17281 Cov.: 32 AF XY: 0.464 AC XY: 34526 AN XY: 74340

African (AFR) AF: 0.627 AC: 26015 AN: 41476

American (AMR) AF: 0.467 AC: 7134 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2803 AN: 5152

South Asian (SAS) AF: 0.524 AC: 2525 AN: 4820

European-Finnish (FIN) AF: 0.379 AC: 4007 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25082 AN: 67984

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.403 Hom.: 41001

Bravo AF: 0.477

Asia WGS AF: 0.554 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.31
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs477077; hg19: chr15-48097117;