15-38055276-A-G

Variant names:

• chr15-38055276-A-G
• rs2382075
• ENST00000558897.1:n.140-4619A>G

Variant summary

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

The ENST00000558897.1(LINC02345):​n.140-4619A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,208 control chromosomes in the GnomAD database, including 2,752 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 0.16 (2752 hom., cov: 32)
• Consequence: LINC02345 ENST00000558897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 3 publications found

Genes affected

LINC02345 (HGNC:53267): (long intergenic non-protein coding RNA 2345)

LINC02895 (HGNC:55422): (long intergenic non-protein coding RNA 2895)

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 = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02345	NR_120330.1	n.140-4619A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02345	ENST00000558897.1	n.140-4619A>G		intron_variant	Intron 2 of 3	3
LINC02345	ENST00000687612.2	n.685-4623A>G		intron_variant	Intron 2 of 2
LINC02895	ENST00000728147.1	n.490-50317T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24779 AN: 152090 Hom.: 2750 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.163 AC: 24807 AN: 152208 Hom.: 2752 Cov.: 32 AF XY: 0.168 AC XY: 12534 AN XY: 74412

African (AFR) AF: 0.116 AC: 4809 AN: 41542

American (AMR) AF: 0.223 AC: 3414 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2865 AN: 5172

South Asian (SAS) AF: 0.407 AC: 1961 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1361 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9329 AN: 68002

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.104 Hom.: 223

Bravo AF: 0.168

Asia WGS AF: 0.420 AC: 1463 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	8.3
DANN	Benign	0.67
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2382075; hg19: chr15-38347477;