ENST00000420049.3:n.610G>C

Variant names:

• chr10-7097556-G-C
• rs3740215
• ENST00000420049.3:n.610G>C

Variant summary

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

The ENST00000420049.3(LINC02665):​n.610G>C variant causes a non coding transcript exon 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: 33)
• Consequence: LINC02665 ENST00000420049.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 1 publications found

Genes affected

LINC02665 (HGNC:54151): (long intergenic non-protein coding RNA 2665)

ENSG00000287277 (HGNC:):

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02665	NR_184104.1	n.534G>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105376387	NR_188183.1	n.190+20724C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02665	ENST00000420049.3	n.610G>C		non_coding_transcript_exon_variant	Exon 3 of 3	3
LINC02665	ENST00000830756.1	n.505G>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287277	ENST00000664549.1	n.190+20724C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.20
DANN	Benign	0.63
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs3740215; hg19: chr10-7139518;