rs12712122

Variant names:

• chr2-101975535-T-A
• rs12712122
• ENST00000627215.2:n.274-8157T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-101975535-T-A
• chr2-101975535-T-C

Variant summary

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

The ENST00000627215.2(LINC01127):​n.274-8157T>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: 29)
• Consequence: LINC01127 ENST00000627215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85
• Publications: 9 publications found

Genes affected

LINC01127 (HGNC:49292): (long intergenic non-protein coding RNA 1127)

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=-1.06).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01127	ENST00000627215.2	n.274-8157T>A		intron_variant	Intron 2 of 2	2
LINC01127	ENST00000627273.3	n.256-8157T>A		intron_variant	Intron 2 of 4	4
LINC01127	ENST00000628502.3	n.248-236T>A		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.019
DANN	Benign	0.25
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs12712122; hg19: chr2-102591997;