rs1301168675

Variant names:

• chr6-17129161-A-C
• NM_001190766.2:c.461A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-17129161-A-C
• chr6-17129161-A-G
• chr6-17129161-A-T

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 𝑓: 0.0000014 (0 hom.)
• Consequence: STMND1 NM_001190766.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.12

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]

ACMG classification

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
STMND1	NM_001190766.2	c.461A>C	p.Lys154Thr	missense_variant	Exon 4 of 5	ENST00000536551.6	NP_001177695.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STMND1	ENST00000536551.6	c.461A>C	p.Lys154Thr	missense_variant	Exon 4 of 5	5	NM_001190766.2	ENSP00000455698.1
STMND1	ENST00000354384.5	c.437A>C	p.Lys146Thr	missense_variant	Exon 4 of 5	5		ENSP00000454363.1
STMND1	ENST00000366215.2	n.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

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;