chr15-47783356-A-G

Position:

• chr15-47783356-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653152.1(LINC01491):​n.619+7751T>C variant causes a intron, non coding transcript 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 ENST00000653152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.619+7751T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.637

Alfa AF: 0.592 Hom.: 4894

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607289; hg19: chr15-48075553;