chr16-25169578-A-T

Variant names:

• chr16-25169578-A-T
• rs277892
• NM_016309.3:c.792+365A>T

Variant summary

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

The NM_016309.3(LCMT1):​c.792+365A>T 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LCMT1 NM_016309.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 2 publications found

Genes affected

LCMT1 (HGNC:17557): (leucine carboxyl methyltransferase 1) LCMT1 catalyzes the methylation of the carboxyl group of the C-terminal leucine residue (leu309) of the catalytic subunit of protein phosphatase-2A (PPP2CA; MIM 176915) (De Baere et al., 1999 [PubMed 10600115]).[supplied by OMIM, Mar 2008]

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016309.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCMT1	NM_016309.3	MANE Select	c.792+365A>T		intron	N/A	NP_057393.2
	LCMT1	NM_001032391.2		c.627+365A>T		intron	N/A	NP_001027563.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCMT1	ENST00000399069.8	TSL:1 MANE Select	c.792+365A>T		intron	N/A	ENSP00000382021.3
	LCMT1	ENST00000380962.9	TSL:2	n.*649+365A>T		intron	N/A	ENSP00000370349.5
	LCMT1	ENST00000380966.8	TSL:2	c.627+365A>T		intron	N/A	ENSP00000370353.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 31932 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16696

African (AFR) AF: 0.00 AC: 0 AN: 1776

American (AMR) AF: 0.00 AC: 0 AN: 2966

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 834

East Asian (EAS) AF: 0.00 AC: 0 AN: 2468

South Asian (SAS) AF: 0.00 AC: 0 AN: 3186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 948

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 102

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18024

Other (OTH) AF: 0.00 AC: 0 AN: 1628

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.68
PhyloP100		0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs277892; hg19: chr16-25180899;