rs337656

Positions:

• chr12-92290575-C-T

Variant summary

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

The ENST00000615716.2(LINC02391):​n.387-17959G>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 0.793 in 152,162 control chromosomes in the GnomAD database, including 47,974 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 0.79 (47974 hom., cov: 31)
• Consequence: LINC02391 ENST00000615716.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02391	XR_007063404.1	n.387-21596G>A		intron_variant, non_coding_transcript_variant
LINC02391	XR_007063403.1	n.387-1968G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02391	ENST00000615716.2	n.387-17959G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120508 AN: 152044 Hom.: 47945 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152162 Hom.: 47974 Cov.: 31 AF XY: 0.797 AC XY: 59279 AN XY: 74380

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.797

Alfa AF: 0.783 Hom.: 66340

Bravo AF: 0.797

Asia WGS AF: 0.928 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337656; hg19: chr12-92684351;