15-38055276-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120330.1(LINC02345):n.140-4619A>G variant causes a intron, non coding transcript 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 NR_120330.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02345	NR_120330.1	n.140-4619A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02345	ENST00000558897.1	n.140-4619A>G		intron_variant, non_coding_transcript_variant		3
LINC02345	ENST00000687612.1	n.198-4623A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.174

Alfa AF: 0.103 Hom.: 217

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2382075; hg19: chr15-38347477;