15-26037644-G-T

Variant names:

• chr15-26037644-G-T
• rs4243761
• ENST00000383019.2:n.896-11481G>T

Variant summary

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

The ENST00000383019.2(LINC02346):​n.896-11481G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,018 control chromosomes in the GnomAD database, including 27,226 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 0.60 (27226 hom., cov: 33)
• Consequence: LINC02346 ENST00000383019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02346	NR_040082.1	n.896-11481G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02346	ENST00000383019.2	n.896-11481G>T		intron_variant	Intron 2 of 4	2
LINC02346	ENST00000659028.1	n.403+8922G>T		intron_variant	Intron 1 of 2
LINC02346	ENST00000659702.1	n.626+8922G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90399 AN: 151900 Hom.: 27194 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.595 AC: 90481 AN: 152018 Hom.: 27226 Cov.: 33 AF XY: 0.596 AC XY: 44298 AN XY: 74286

African (AFR) AF: 0.672 AC: 27873 AN: 41462

American (AMR) AF: 0.551 AC: 8421 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1825 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4156 AN: 5180

South Asian (SAS) AF: 0.610 AC: 2934 AN: 4810

European-Finnish (FIN) AF: 0.539 AC: 5676 AN: 10538

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37703 AN: 67970

Other (OTH) AF: 0.583 AC: 1233 AN: 2114

Alfa AF: 0.569 Hom.: 43437

Bravo AF: 0.600

Asia WGS AF: 0.704 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs4243761; hg19: chr15-26282791;