rs12037513

Positions:

• chr1-25898142-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145454.3(STMN1):​c.378+3349T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,110 control chromosomes in the GnomAD database, including 10,172 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 0.36 (10172 hom., cov: 32)
• Consequence: STMN1 NM_001145454.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STMN1	NM_001145454.3	c.378+3349T>C		intron_variant			NP_001138926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STMN1	ENST00000426559.6	c.378+3349T>C		intron_variant		1		ENSP00000410452.2

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54398 AN: 151992 Hom.: 10151 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.329

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 54449 AN: 152110 Hom.: 10172 Cov.: 32 AF XY: 0.356 AC XY: 26500 AN XY: 74370

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.333

Alfa AF: 0.314 Hom.: 10725

Bravo AF: 0.351

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12037513; hg19: chr1-26224633;