rs1318900623

Variant names:

• chr6-17129119-C-T
• rs1318900623
• NM_001190766.2:c.419C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001190766.2(STMND1):​c.419C>T​(p.Thr140Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000578 in 1,383,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000058 (0 hom.)
• Consequence: STMND1 NM_001190766.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.821
• Publications: 1 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12132186).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001190766.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STMND1	NM_001190766.2	MANE Select	c.419C>T	p.Thr140Met	missense	Exon 4 of 5	NP_001177695.1	H3BQB6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STMND1	ENST00000536551.6	TSL:5 MANE Select	c.419C>T	p.Thr140Met	missense	Exon 4 of 5	ENSP00000455698.1	H3BQB6
	STMND1	ENST00000907738.1		c.413C>T	p.Thr138Met	missense	Exon 4 of 5	ENSP00000577797.1
	STMND1	ENST00000354384.5	TSL:5	c.395C>T	p.Thr132Met	missense	Exon 4 of 5	ENSP00000454363.1	H3BMF7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000744 AC: 1 AN: 134406 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000189

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000578 AC: 8 AN: 1383182 Hom.: 0 Cov.: 30 AF XY: 0.00000586 AC XY: 4 AN XY: 682548

African (AFR) AF: 0.0000317 AC: 1 AN: 31572

American (AMR) AF: 0.00 AC: 0 AN: 35652

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25158

East Asian (EAS) AF: 0.00 AC: 0 AN: 35702

South Asian (SAS) AF: 0.0000126 AC: 1 AN: 79192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33848

Middle Eastern (MID) AF: 0.000176 AC: 1 AN: 5696

European-Non Finnish (NFE) AF: 0.00000464 AC: 5 AN: 1078506

Other (OTH) AF: 0.00 AC: 0 AN: 57856

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	5.2
DANN	Benign	0.80
DEOGEN2	Benign	0.035	T
FATHMM_MKL	Benign	0.0099	N
LIST_S2	Benign	0.42	T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.12	T
MutationAssessor	Benign	0.20	N
PhyloP100		-0.82
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-3.0	D
Sift	Benign	0.092	T
Sift4G	Benign	0.082	T
Vest4		0.069
MVP		0.20
GERP RS		-2.2
Varity_R		0.028
gMVP		0.11
Mutation Taster		=95/5	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1318900623; hg19: chr6-17129350; COSMIC: COSV104670657;