chr15-26033742-T-C

Variant names:

• chr15-26033742-T-C
• rs11633924
• ENST00000383019.2:n.896-15383T>C

Variant summary

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

The ENST00000383019.2(LINC02346):​n.896-15383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,040 control chromosomes in the GnomAD database, including 28,766 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 0.61 (28766 hom., cov: 32)
• Consequence: LINC02346 ENST00000383019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02346	NR_040082.1	n.896-15383T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02346	ENST00000383019.2	n.896-15383T>C		intron_variant	Intron 2 of 4	2
LINC02346	ENST00000659028.1	n.403+5020T>C		intron_variant	Intron 1 of 2
LINC02346	ENST00000659702.1	n.626+5020T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92775 AN: 151922 Hom.: 28718 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.611 AC: 92880 AN: 152040 Hom.: 28766 Cov.: 32 AF XY: 0.618 AC XY: 45893 AN XY: 74282

African (AFR) AF: 0.688 AC: 28523 AN: 41480

American (AMR) AF: 0.592 AC: 9045 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3468

East Asian (EAS) AF: 0.821 AC: 4219 AN: 5136

South Asian (SAS) AF: 0.650 AC: 3124 AN: 4808

European-Finnish (FIN) AF: 0.624 AC: 6603 AN: 10574

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

European-Non Finnish (NFE) AF: 0.551 AC: 37469 AN: 67982

Other (OTH) AF: 0.595 AC: 1254 AN: 2108

Alfa AF: 0.573 Hom.: 9451

Bravo AF: 0.610

Asia WGS AF: 0.741 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.30
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11633924; hg19: chr15-26278889;