12-3322405-C-T

Variant names:

• chr12-3322405-C-T
• rs1978238
• NR_187484.1:n.4487C>T

Variant summary

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

The NR_187484.1(LINC02827):​n.4487C>T 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: LINC02827 NR_187484.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

Genes affected

LINC02827 (HGNC:54358): (long intergenic non-protein coding RNA 2827)

ENSG00000250770 (HGNC:):

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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02827	NR_187484.1	n.4487C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC100128253	NR_148995.1	n.65-14587G>A		intron_variant	Intron 1 of 11
LINC02827	NR_187482.1	n.1609-944C>T		intron_variant	Intron 5 of 5
LINC02827	NR_187483.1	n.1982-944C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02827	ENST00000432994.2	n.1010-944C>T		intron_variant	Intron 1 of 1	2
LINC02827	ENST00000543036.1	n.287-944C>T		intron_variant	Intron 1 of 2	2
ENSG00000250770	ENST00000635814.1	n.273+919G>A		intron_variant	Intron 2 of 6	6

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	-0.88
CADD	Benign	4.6
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978238; hg19: chr12-3431571;