rs1146030

Variant names:

• chr2-161248273-C-A
• rs1146030
• ENST00000436506.5:n.1700C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-161248273-C-A
• chr2-161248273-C-G
• chr2-161248273-C-T

Variant summary

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

The ENST00000436506.5(LINC01806):​n.1700C>A 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: LINC01806 ENST00000436506.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 2 publications found

Genes affected

LINC01806 (HGNC:52599): (long intergenic non-protein coding RNA 1806)

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

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=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01806	NR_110163.1	n.1600C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01806	NR_110164.1	n.1556C>A		non_coding_transcript_exon_variant	Exon 2 of 2
PSMD14-DT	NR_110593.1	n.348+251G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01806	ENST00000436506.5	n.1700C>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC01806	ENST00000439050.2	n.1576C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC01806	ENST00000655684.3	n.1622C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 2885

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.31
DANN	Benign	0.11
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1146030; hg19: chr2-162104784;