rs727504798

chr12-98537585-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The ENST00000261210.9(TMPO):c.676T>G(p.Leu226Val) variant causes a missense 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. 12/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TMPO ENST00000261210.9 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.304

Genes affected

TMPO (HGNC:11875): (thymopoietin) Through alternative splicing, this gene encodes several distinct LEM domain containing protein isoforms. LEM domain proteins include inner nuclear membrane and intranuclear proteins, and are involved in a variety of cellular functions including gene expression, chromatin organization, and replication and cell cycle control. The encoded alpha isoform is broadly diffuse in the nucleus and contains a lamin binding domain, while the beta and gamma isoforms are localized to the nuclear membrane and contain an HDAC3 interaction domain. The distinct isoforms may compete with each other when acting to chaperone other proteins and regulate transcription. [provided by RefSeq, Aug 2019]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.050140917).
• BP6: Variant 12-98537585-T-G is Benign according to our data. Variant chr12-98537585-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 179335.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMPO	NM_001032283.3	c.663+13T>G		intron_variant		ENST00000556029.6
TMPO	NM_001032284.3	c.663+13T>G		intron_variant
TMPO	NM_001307975.2	c.663+13T>G		intron_variant
TMPO	XM_005269132.5	c.663+13T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMPO	ENST00000556029.6	c.663+13T>G		intron_variant		1	NM_001032283.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 01, 2013

633+13T>G in intron 4 of TMPO: This variant is not expected to have clinical sig nificance because it is not located within the splice consensus sequence. 633+1 3T>G in intron 4 of TMPO (allele frequency = n/a) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
Cadd	Benign	12
Dann	Benign	0.23
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.29	T
M_CAP	Benign	0.025	T
MetaRNN	Benign	0.050	T
MetaSVM	Benign	-0.99	T
MutationTaster	Benign	1.0	N;N;N;N
PROVEAN	Benign	0.20	N
REVEL	Benign	0.086
Sift	Benign	0.13	T
Sift4G	Benign	0.36	T
Vest4		0.16
MutPred		0.21		Gain of sheet (P = 0.1451);
MVP		0.20
ClinPred		0.044	T
GERP RS		-0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727504798; hg19: chr12-98931363;