rs7525939

Positions:

• chr1-226568270-C-T

Variant summary

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

The NM_001003665.4(STUM):​c.202+19164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,018 control chromosomes in the GnomAD database, including 3,652 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 0.18 (3652 hom., cov: 32)
• Consequence: STUM NM_001003665.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

STUM (HGNC:30491): (stum, mechanosensory transduction mediator homolog) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STUM	NM_001003665.4	c.202+19164C>T		intron_variant		ENST00000366788.8
STUM	NM_001410930.1	c.202+19164C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STUM	ENST00000366788.8	c.202+19164C>T		intron_variant		5	NM_001003665.4	P4
STUM	ENST00000366789.6	c.202+19164C>T		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27595 AN: 151900 Hom.: 3649 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0831

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.182 AC: 27616 AN: 152018 Hom.: 3652 Cov.: 32 AF XY: 0.179 AC XY: 13274 AN XY: 74336

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0831

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.149

Alfa AF: 0.128 Hom.: 805

Bravo AF: 0.188

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.38
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7525939; hg19: chr1-226755971;