NM_001003665.4:c.202+19164C>T

Variant names:

• chr1-226568270-C-T
• rs7525939
• NM_001003665.4:c.202+19164C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STUM	NM_001003665.4	c.202+19164C>T		intron_variant	Intron 1 of 3	ENST00000366788.8	NP_001003665.1
STUM	NM_001410930.1	c.202+19164C>T		intron_variant	Intron 1 of 2		NP_001397859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STUM	ENST00000366788.8	c.202+19164C>T		intron_variant	Intron 1 of 3	5	NM_001003665.4	ENSP00000355752.3
STUM	ENST00000366789.6	c.202+19164C>T		intron_variant	Intron 1 of 2	5		ENSP00000355753.5

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

African (AFR) AF: 0.379 AC: 15698 AN: 41442

American (AMR) AF: 0.104 AC: 1594 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0831 AC: 288 AN: 3466

East Asian (EAS) AF: 0.125 AC: 648 AN: 5170

South Asian (SAS) AF: 0.152 AC: 729 AN: 4810

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7095 AN: 67952

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.126 Hom.: 861

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
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7525939; hg19: chr1-226755971;