NM_032780.4:c.897G>T

Variant names:

• chr11-118534089-G-T
• rs6589664
• NM_032780.4:c.897G>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_032780.4(TMEM25):​c.897G>T​(p.Pro299Pro) variant causes a synonymous 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: 31)
• Consequence: TMEM25 NM_032780.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 28 publications found

Genes affected

TMEM25 (HGNC:25890): (transmembrane protein 25) Predicted to be involved in negative regulation of excitatory postsynaptic potential and regulation of protein stability. Predicted to be located in late endosome and lysosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.011).
• BP7: Synonymous conserved (PhyloP=-2.7 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032780.4. 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
	TMEM25	NM_032780.4	MANE Select	c.897G>T	p.Pro299Pro	synonymous	Exon 7 of 9	NP_116169.2
	TMEM25	NM_001318755.2		c.897G>T	p.Pro299Pro	synonymous	Exon 7 of 9	NP_001305684.1
	TMEM25	NM_001144037.2		c.897G>T	p.Pro299Pro	synonymous	Exon 7 of 9	NP_001137509.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM25	ENST00000313236.10	TSL:1 MANE Select	c.897G>T	p.Pro299Pro	synonymous	Exon 7 of 9	ENSP00000315635.5
	TMEM25	ENST00000533102.5	TSL:1	c.897G>T	p.Pro299Pro	synonymous	Exon 7 of 9	ENSP00000431548.1
	TMEM25	ENST00000359862.8	TSL:1	c.765G>T	p.Pro255Pro	synonymous	Exon 6 of 8	ENSP00000352924.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 46

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.16
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6589664; hg19: chr11-118404804;