rs454217

chr12-92324782-C-T

Variant summary

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

The ENST00000615716.2(LINC02391):n.386+32749G>A 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 0.657 in 152,032 control chromosomes in the GnomAD database, including 33,769 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 0.66 (33769 hom., cov: 31)
• Consequence: LINC02391 ENST00000615716.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

LINC02391 (HGNC:53318): (long intergenic non-protein coding RNA 2391)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02391	XR_007063404.1	n.386+32749G>A		intron_variant, non_coding_transcript_variant
LINC02391	XR_007063403.1	n.386+32749G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02391	ENST00000615716.2	n.386+32749G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99748 AN: 151914 Hom.: 33725 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.657 AC: 99858 AN: 152032 Hom.: 33769 Cov.: 31 AF XY: 0.653 AC XY: 48508 AN XY: 74312

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.638

Alfa AF: 0.623 Hom.: 5094

Bravo AF: 0.666

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.9
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs454217; hg19: chr12-92718558;