rs938076

Variant names:

• chr15-25987772-G-A
• rs938076
• ENST00000383019.2:n.208-27562G>A

Variant summary

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

The ENST00000383019.2(LINC02346):​n.208-27562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,068 control chromosomes in the GnomAD database, including 9,923 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 0.32 (9923 hom., cov: 32)
• Consequence: LINC02346 ENST00000383019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02346	NR_040082.1	n.208-27562G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02346	ENST00000383019.2	n.208-27562G>A		intron_variant	Intron 1 of 4	2
LINC02346	ENST00000654579.1	n.151-27562G>A		intron_variant	Intron 1 of 1
LINC02346	ENST00000659702.1	n.445-40769G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49150 AN: 151950 Hom.: 9917 Cov.: 32

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.323 AC: 49175 AN: 152068 Hom.: 9923 Cov.: 32 AF XY: 0.321 AC XY: 23874 AN XY: 74318

African (AFR) AF: 0.0936 AC: 3887 AN: 41520

American (AMR) AF: 0.382 AC: 5831 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.136 AC: 705 AN: 5172

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5129 AN: 10556

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30201 AN: 67952

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.404 Hom.: 7250

Bravo AF: 0.308

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.89
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs938076; hg19: chr15-26232919;