rs2373038

chr14-85947936-G-A

Variant summary

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

The NR_110155.1(LINC02328):n.184+13075G>A 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 0.343 in 151,874 control chromosomes in the GnomAD database, including 9,145 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 0.34 (9145 hom., cov: 32)
• Consequence: LINC02328 NR_110155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02328	NR_110155.1	n.184+13075G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02328	ENST00000668344.3	n.253+13075G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52027 AN: 151752 Hom.: 9144 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.343 AC: 52040 AN: 151874 Hom.: 9145 Cov.: 32 AF XY: 0.341 AC XY: 25294 AN XY: 74198

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.349

Alfa AF: 0.354 Hom.: 12924

Bravo AF: 0.339

Asia WGS AF: 0.384 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.72
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: rs2373038; hg19: chr14-86414280;