ENST00000557195.5:n.152+13075G>A

Variant names:

• chr14-85947936-G-A
• rs2373038
• ENST00000557195.5:n.152+13075G>A

Variant summary

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

The ENST00000557195.5(LINC02328):​n.152+13075G>A variant causes a intron 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 ENST00000557195.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557195.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	NR_110155.1		n.184+13075G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	ENST00000557195.5	TSL:3	n.152+13075G>A		intron	N/A
	LINC02328	ENST00000654590.3		n.289+13075G>A		intron	N/A
	LINC02328	ENST00000654941.1		n.236+13075G>A		intron	N/A

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

African (AFR) AF: 0.337 AC: 13953 AN: 41426

American (AMR) AF: 0.299 AC: 4545 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1889 AN: 5154

South Asian (SAS) AF: 0.428 AC: 2060 AN: 4816

European-Finnish (FIN) AF: 0.319 AC: 3363 AN: 10540

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23581 AN: 67946

Other (OTH) AF: 0.349 AC: 734 AN: 2104

Alfa AF: 0.353 Hom.: 16168

Bravo AF: 0.339

Asia WGS AF: 0.384 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.67
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2373038; hg19: chr14-86414280;