6-29507365-C-G

Variant names:

• chr6-29507365-C-G
• rs734960
• ENST00000436804.3:n.321C>G

Variant summary

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

The ENST00000436804.3(LINC02829):​n.321C>G 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: 32)
• Consequence: LINC02829 ENST00000436804.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 13 publications found

Genes affected

LINC02829 (HGNC:54362): (long intergenic non-protein coding RNA 2829)

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02829	NR_183359.1	n.319C>G		non_coding_transcript_exon_variant	Exon 3 of 4
LINC02829	NR_183360.1	n.387C>G		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000436804.3	n.321C>G		non_coding_transcript_exon_variant	Exon 3 of 4	5
LINC02829	ENST00000661850.2	n.450C>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02829	ENST00000824900.1	n.389C>G		non_coding_transcript_exon_variant	Exon 4 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs734960; hg19: chr6-29475142;