NM_007029.4:c.101T>G

Variant names:

• chr8-79636883-T-G
• rs1012795099
• NM_007029.4:c.101T>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_007029.4(STMN2):​c.101T>G​(p.Ile34Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I34T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: STMN2 NM_007029.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.57

Genes affected

STMN2 (HGNC:10577): (stathmin 2) This gene encodes a member of the stathmin family of phosphoproteins. Stathmin proteins function in microtubule dynamics and signal transduction. The encoded protein plays a regulatory role in neuronal growth and is also thought to be involved in osteogenesis. Reductions in the expression of this gene have been associated with Down's syndrome and Alzheimer's disease. Alternatively spliced transcript variants have been observed for this gene. A pseudogene of this gene is located on the long arm of chromosome 6. [provided by RefSeq, Nov 2010]

LOC105375916 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.32191598).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STMN2	NM_007029.4	c.101T>G	p.Ile34Ser	missense_variant	Exon 2 of 5	ENST00000220876.12	NP_008960.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STMN2	ENST00000220876.12	c.101T>G	p.Ile34Ser	missense_variant	Exon 2 of 5	1	NM_007029.4	ENSP00000220876.7
STMN2	ENST00000518111.5	c.101T>G	p.Ile34Ser	missense_variant	Exon 2 of 6	3		ENSP00000429243.1
STMN2	ENST00000518491.1	c.68T>G	p.Ile23Ser	missense_variant	Exon 2 of 5	2		ENSP00000430102.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.015	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	22
DANN	Benign	0.93
DEOGEN2	Benign	0.23	T;.;T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.040
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.69	T;T;T
M_CAP	Benign	0.0074	T
MetaRNN	Benign	0.32	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L;L;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-1.9	N;N;N
REVEL	Benign	0.16
Sift	Benign	0.49	T;T;T
Sift4G	Benign	0.21	T;T;T
Polyphen		0.0080	B;.;.
Vest4		0.54
MutPred		0.44		Loss of stability (P = 0.0141);Loss of stability (P = 0.0141);.;
MVP		0.35
MPC		1.4
ClinPred		0.40	T
GERP RS		5.7
Varity_R		0.23
gMVP		0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012795099; hg19: chr8-80549118;