dbSNP rs213641: STMN1:c.-63+524G>T (chr1-25905865-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005563.4(STMN1):c.-63+524G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,194 control chromosomes in the GnomAD database, including 32,773 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 32745 hom., cov: 34)

Exomes 𝑓: 0.69 ( 28 hom. )

Consequence

STMN1
NM_005563.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.142

Publications

13 publications found

Variant links:

Genes affected

STMN1 (HGNC:6510): (stathmin 1) This gene belongs to the stathmin family of genes. It encodes a ubiquitous cytosolic phosphoprotein proposed to function as an intracellular relay integrating regulatory signals of the cellular environment. The encoded protein is involved in the regulation of the microtubule filament system by destabilizing microtubules. It prevents assembly and promotes disassembly of microtubules. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

STMN1 links:

ENSG00000294297 (HGNC:):

ENSG00000294297 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STMN1	NM_005563.4 link	c.-63+524G>T		intron_variant	Intron 1 of 4	ENST00000455785.7	NP_005554.1	P16949-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STMN1	ENST00000455785.7 link	c.-63+524G>T		intron_variant	Intron 1 of 4	1	NM_005563.4	ENSP00000387858.2		P16949-1

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98488

AN:

151952

Hom.:

32683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.772

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.669

Gnomad SAS

AF:

0.753

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.618

GnomAD4 exome

AF:

0.694

AC:

AN:

124

Hom.:

Cov.:

AF XY:

0.708

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.857

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.649

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.648

AC:

98614

AN:

152070

Hom.:

32745

Cov.:

AF XY:

0.648

AC XY:

48173

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.772

AC:

32046

AN:

41514

American (AMR)

AF:

0.684

AC:

10463

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

1627

AN:

3468

East Asian (EAS)

AF:

0.669

AC:

3428

AN:

5124

South Asian (SAS)

AF:

0.754

AC:

3635

AN:

4824

European-Finnish (FIN)

AF:

0.522

AC:

5531

AN:

10590

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.588

AC:

39947

AN:

67946

Other (OTH)

AF:

0.618

AC:

1302

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1741

3482

5222

6963

8704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.638

Hom.:

8641

Bravo

AF:

0.660

Asia WGS

AF:

0.758

AC:

2637

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.3

(source)

DANN

Benign

0.77

PhyloP100

-0.14

PromoterAI

0.042

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over