ENST00000534675.1:n.64+3142T>C

Variant names:

• chr8-81888582-T-C
• rs1452001
• ENST00000534675.1:n.64+3142T>C

Variant summary

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

The ENST00000534675.1(LINC02235):​n.64+3142T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,048 control chromosomes in the GnomAD database, including 28,917 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 0.61 (28917 hom., cov: 32)
• Consequence: LINC02235 ENST00000534675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 11 publications found

Genes affected

LINC02235 (HGNC:53106): (long intergenic non-protein coding RNA 2235)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534675.1. 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
	LINC02235	NR_170313.1		n.280+14206T>C		intron	N/A
	LINC02235	NR_170314.1		n.340+15064T>C		intron	N/A
	LINC02235	NR_170315.1		n.389+15064T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02235	ENST00000534675.1	TSL:5	n.64+3142T>C		intron	N/A
	LINC02235	ENST00000647805.1		n.871+15064T>C		intron	N/A
	LINC02235	ENST00000655672.1		n.301+15064T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92681 AN: 151928 Hom.: 28896 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.610 AC: 92749 AN: 152048 Hom.: 28917 Cov.: 32 AF XY: 0.616 AC XY: 45813 AN XY: 74318

African (AFR) AF: 0.553 AC: 22940 AN: 41480

American (AMR) AF: 0.651 AC: 9933 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3472

East Asian (EAS) AF: 0.980 AC: 5065 AN: 5168

South Asian (SAS) AF: 0.643 AC: 3105 AN: 4832

European-Finnish (FIN) AF: 0.717 AC: 7586 AN: 10582

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40035 AN: 67944

Other (OTH) AF: 0.597 AC: 1254 AN: 2102

Alfa AF: 0.597 Hom.: 13936

Bravo AF: 0.606

Asia WGS AF: 0.811 AC: 2817 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs1452001; hg19: chr8-82800817;