rs67666182

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-81859802-A-C
• chr8-81859802-A-G
• chr8-81859802-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_170313.1(LINC02235):​n.54-13600A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LINC02235 NR_170313.1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.45
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;