ENST00000647805.1:n.754+5966A>G

Variant names:

• chr8-81859802-A-G
• rs67666182
• ENST00000647805.1:n.754+5966A>G

Variant summary

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

The ENST00000647805.1(LINC02235):​n.754+5966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,064 control chromosomes in the GnomAD database, including 9,541 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 0.35 (9541 hom., cov: 32)
• Consequence: LINC02235 ENST00000647805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647805.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02235	NR_170313.1		n.54-13600A>G		intron	N/A
	LINC02235	NR_170314.1		n.223+10695A>G		intron	N/A
	LINC02235	NR_170315.1		n.273-13600A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02235	ENST00000647805.1		n.754+5966A>G		intron	N/A
	LINC02235	ENST00000655672.1		n.185-13600A>G		intron	N/A
	LINC02235	ENST00000658926.1		n.366+5966A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52865 AN: 151946 Hom.: 9531 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.348 AC: 52892 AN: 152064 Hom.: 9541 Cov.: 32 AF XY: 0.348 AC XY: 25859 AN XY: 74308

African (AFR) AF: 0.371 AC: 15402 AN: 41482

American (AMR) AF: 0.354 AC: 5414 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3115 AN: 5148

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4824

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10586

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21688 AN: 67962

Other (OTH) AF: 0.352 AC: 742 AN: 2108

Alfa AF: 0.326 Hom.: 1065

Bravo AF: 0.356

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs67666182; hg19: chr8-82772037;