1-25893357-A-G

Position:

• chr1-25893357-A-G

Variant summary

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

The ENST00000426559.6(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 ENST00000426559.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STMN1	NM_001145454.3	c.379-7488T>C		intron_variant			NP_001138926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STMN1	ENST00000426559.6	c.379-7488T>C		intron_variant		1		ENSP00000410452

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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.564

Alfa AF: 0.559 Hom.: 11033

Bravo AF: 0.563

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159522; hg19: chr1-26219848;