15-26032398-A-G

Position:

• chr15-26032398-A-G

Variant summary

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

The NR_040082.1(LINC02346):​n.895+16377A>G 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 0.583 in 151,976 control chromosomes in the GnomAD database, including 25,960 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 0.58 (25960 hom., cov: 32)
• Consequence: LINC02346 NR_040082.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

LINC02346 (HGNC:53268): (long intergenic non-protein coding RNA 2346)

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 = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02346	NR_040082.1	n.895+16377A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02346	ENST00000659702.1	n.626+3676A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88495 AN: 151858 Hom.: 25922 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.583 AC: 88587 AN: 151976 Hom.: 25960 Cov.: 32 AF XY: 0.592 AC XY: 43962 AN XY: 74252

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.577

Alfa AF: 0.566 Hom.: 25579

Bravo AF: 0.579

Asia WGS AF: 0.731 AC: 2542 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	5.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4906844; hg19: chr15-26277545;