10-61851595-C-G

Variant names:

• chr10-61851595-C-G
• rs2588969
• ENST00000717519.1:n.214+11866G>C

Variant summary

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

The ENST00000717519.1(LINC02625):​n.214+11866G>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: 30)
• Consequence: LINC02625 ENST00000717519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 16 publications found

Genes affected

LINC02625 (HGNC:54104): (long intergenic non-protein coding RNA 2625)

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=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02625	XR_001747458.2	n.184+11866G>C		intron_variant	Intron 2 of 5
LINC02625	XR_001747460.2	n.303+11866G>C		intron_variant	Intron 2 of 5
LINC02625	XR_001747461.2	n.187+11866G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02625	ENST00000717519.1	n.214+11866G>C		intron_variant	Intron 2 of 3
LINC02625	ENST00000717534.1	n.217+11866G>C		intron_variant	Intron 2 of 3
LINC02625	ENST00000717535.1	n.373+11866G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.58
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2588969; hg19: chr10-63611354;