chr8-81889368-A-G

Variant names:

• chr8-81889368-A-G
• rs1452002
• ENST00000534675.1:n.64+3928A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_170313.1(LINC02235):​n.280+14992A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,070 control chromosomes in the GnomAD database, including 19,755 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 0.48 (19755 hom., cov: 32)
• Consequence: LINC02235 NR_170313.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_170313.1. 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.280+14992A>G		intron	N/A
	LINC02235	NR_170314.1		n.340+15850A>G		intron	N/A
	LINC02235	NR_170315.1		n.389+15850A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02235	ENST00000534675.1	TSL:5	n.64+3928A>G		intron	N/A
	LINC02235	ENST00000647805.1		n.871+15850A>G		intron	N/A
	LINC02235	ENST00000655672.1		n.301+15850A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73630 AN: 151952 Hom.: 19750 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.484 AC: 73673 AN: 152070 Hom.: 19755 Cov.: 32 AF XY: 0.495 AC XY: 36772 AN XY: 74324

African (AFR) AF: 0.275 AC: 11397 AN: 41494

American (AMR) AF: 0.562 AC: 8582 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5071 AN: 5178

South Asian (SAS) AF: 0.561 AC: 2705 AN: 4826

European-Finnish (FIN) AF: 0.668 AC: 7064 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35358 AN: 67952

Other (OTH) AF: 0.481 AC: 1016 AN: 2112

Alfa AF: 0.511 Hom.: 10332

Bravo AF: 0.472

Asia WGS AF: 0.761 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.77
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1452002; hg19: chr8-82801603;