12-131352932-A-T

Variant names:

• chr12-131352932-A-T
• rs4255618
• ENST00000659569.1:n.496T>A

Variant summary

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

The ENST00000659569.1(ENSG00000287792):​n.496T>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: 34)
• Consequence: ENSG00000287792 ENST00000659569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 1 publications found

Genes affected

ENSG00000287792 (HGNC:):

LINC02370 (HGNC:27885): (long intergenic non-protein coding RNA 2370)

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=-1.24).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02370	NR_103736.1	n.409+3388A>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287792	ENST00000659569.1	n.496T>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02370	ENST00000428272.4	n.409+3388A>T		intron_variant	Intron 2 of 2	5
LINC02370	ENST00000743505.1	n.1164+5271A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4255618; hg19: chr12-131837477;