rs1301168675

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001190766.2(STMND1):​c.461A>C​(p.Lys154Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000145 in 1,383,734 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. K154I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

STMND1
NM_001190766.2 missense

Scores

1
9
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.12
Variant links:
Genes affected
STMND1 (HGNC:44668): (stathmin domain containing 1) Predicted to enable tubulin binding activity. Predicted to be involved in microtubule depolymerization; neuron projection development; and regulation of microtubule polymerization or depolymerization. Predicted to be active in cytoplasm and neuron projection. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STMND1NM_001190766.2 linkc.461A>C p.Lys154Thr missense_variant Exon 4 of 5 ENST00000536551.6 NP_001177695.1 H3BQB6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STMND1ENST00000536551.6 linkc.461A>C p.Lys154Thr missense_variant Exon 4 of 5 5 NM_001190766.2 ENSP00000455698.1 H3BQB6
STMND1ENST00000354384.5 linkc.437A>C p.Lys146Thr missense_variant Exon 4 of 5 5 ENSP00000454363.1 H3BMF7
STMND1ENST00000366215.2 linkn.1224A>C non_coding_transcript_exon_variant Exon 1 of 2 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000145
AC:
2
AN:
1383734
Hom.:
0
Cov.:
30
AF XY:
0.00000146
AC XY:
1
AN XY:
682804
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000185
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Uncertain
0.024
T
BayesDel_noAF
Benign
-0.20
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.19
T;.
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.78
T;T
M_CAP
Uncertain
0.16
D
MetaRNN
Uncertain
0.43
T;T
MutationAssessor
Uncertain
2.2
M;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Uncertain
-4.1
D;D
Sift
Uncertain
0.014
D;D
Sift4G
Pathogenic
0.0
D;D
Vest4
0.42
MVP
0.31
GERP RS
5.8
Varity_R
0.29
gMVP
0.064

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-17129392; API