rs1766163

Variant names:

• chr1-90848953-T-A
• rs1766163
• ENST00000443802.4:n.189+2530A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-90848953-T-A
• chr1-90848953-T-C

Variant summary

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

The ENST00000443802.4(LINC02609):​n.189+2530A>T 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: LINC02609 ENST00000443802.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 4 publications found

Genes affected

LINC02609 (HGNC:27140): (long intergenic non-protein coding RNA 2609)

LINC02788 (HGNC:54309): (long intergenic non-protein coding RNA 2788)

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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443802.4. 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
	LINC02609	NR_135038.1		n.156+2530A>T		intron	N/A
	LINC02609	NR_147930.1		n.168+2530A>T		intron	N/A
	LINC02609	NR_147931.1		n.168+2530A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	ENST00000443802.4	TSL:3	n.189+2530A>T		intron	N/A
	LINC02609	ENST00000606660.1	TSL:2	n.136+2530A>T		intron	N/A
	LINC02609	ENST00000634619.2	TSL:5	n.165+2530A>T		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

Alfa AF: 0.00 Hom.: 14499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.67
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1766163; hg19: chr1-91314510;