chr2-19494439-C-A

Variant names:

• chr2-19494439-C-A
• rs6705213
• ENST00000641680.1:n.530+5950C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_183418.1(LINC01808):​n.605+5950C>A 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: LINC01808 NR_183418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

Genes affected

LINC01808 (HGNC:52611): (long intergenic non-protein coding RNA 1808)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01808	NR_183418.1	n.605+5950C>A		intron_variant	Intron 5 of 5
LINC01808	NR_183420.1	n.544+5950C>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01808	ENST00000641680.1	n.530+5950C>A		intron_variant	Intron 5 of 5
LINC01808	ENST00000641932.1	n.1194+5950C>A		intron_variant	Intron 6 of 6
LINC01808	ENST00000657829.1	n.649+5950C>A		intron_variant	Intron 5 of 5
LINC01808	ENST00000670653.1	n.811+5950C>A		intron_variant	Intron 4 of 4

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	-1.0
CADD	Benign	0.048
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6705213; hg19: chr2-19694200;