15-26032398-A-G

Variant names:

• chr15-26032398-A-G
• rs4906844
• ENST00000383019.2:n.895+16377A>G

Variant summary

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

The ENST00000383019.2(LINC02346):​n.895+16377A>G variant causes a intron 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 ENST00000383019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02346	NR_040082.1	n.895+16377A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02346	ENST00000383019.2	n.895+16377A>G		intron_variant	Intron 2 of 4	2
LINC02346	ENST00000659028.1	n.403+3676A>G		intron_variant	Intron 1 of 2
LINC02346	ENST00000659702.1	n.626+3676A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.591 AC: 24494 AN: 41450

American (AMR) AF: 0.582 AC: 8897 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4222 AN: 5148

South Asian (SAS) AF: 0.647 AC: 3114 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6585 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37409 AN: 67934

Other (OTH) AF: 0.577 AC: 1218 AN: 2110

Alfa AF: 0.565 Hom.: 71601

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4906844; hg19: chr15-26277545;