1-25893357-A-G

Variant names:

• chr1-25893357-A-G
• rs159522
• ENST00000426559.7:c.379-7488T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426559.7(STMN1):​c.379-7488T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,872 control chromosomes in the GnomAD database, including 24,066 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 0.56 (24066 hom., cov: 31)
• Consequence: STMN1 ENST00000426559.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426559.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STMN1	NM_001145454.3		c.379-7488T>C		intron	N/A	NP_001138926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STMN1	ENST00000426559.7	TSL:1	c.379-7488T>C		intron	N/A	ENSP00000410452.2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84911 AN: 151752 Hom.: 24024 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.560 AC: 85012 AN: 151872 Hom.: 24066 Cov.: 31 AF XY: 0.561 AC XY: 41644 AN XY: 74208

African (AFR) AF: 0.541 AC: 22395 AN: 41360

American (AMR) AF: 0.643 AC: 9820 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3466 AN: 5168

South Asian (SAS) AF: 0.744 AC: 3581 AN: 4810

European-Finnish (FIN) AF: 0.483 AC: 5091 AN: 10534

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37243 AN: 67952

Other (OTH) AF: 0.564 AC: 1192 AN: 2114

Alfa AF: 0.558 Hom.: 12179

Bravo AF: 0.563

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.69
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs159522; hg19: chr1-26219848;