chr1-121458637-G-C

Variant names:

• chr1-121458637-G-C
• rs6600671
• ENST00000417218.2:n.1066-1382G>C

Variant summary

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

The ENST00000417218.2(LINC02798):​n.1066-1382G>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: LINC02798 ENST00000417218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 0 publications found

Genes affected

LINC02798 (HGNC:54323): (long intergenic non-protein coding RNA 2798)

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02798	XM_047438024.1	c.*378-1382G>C		intron_variant	Intron 1 of 1		XP_047293980.1
LINC02798	XR_007066532.1	n.826-1382G>C		intron_variant	Intron 2 of 2
LINC02798	XR_007066534.1	n.550-1382G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02798	ENST00000417218.2	n.1066-1382G>C		intron_variant	Intron 1 of 1	1
LINC02798	ENST00000650414.1	n.596-1382G>C		intron_variant	Intron 3 of 3
LINC02798	ENST00000664311.1	n.330-1382G>C		intron_variant	Intron 2 of 2

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6600671; hg19: chr1-121200490;