rs708755

Variant names:

• chr1-226598882-G-A
• rs708755
• NM_001003665.4:c.383-1784G>A

Variant summary

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

The NM_001003665.4(STUM):​c.383-1784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,176 control chromosomes in the GnomAD database, including 1,258 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 0.10 (1258 hom., cov: 33)
• Consequence: STUM NM_001003665.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STUM	NM_001003665.4	c.383-1784G>A		intron_variant	Intron 2 of 3	ENST00000366788.8	NP_001003665.1
STUM	NM_001410930.1	c.382+1901G>A		intron_variant	Intron 2 of 2		NP_001397859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STUM	ENST00000366788.8	c.383-1784G>A		intron_variant	Intron 2 of 3	5	NM_001003665.4	ENSP00000355752.3
STUM	ENST00000366789.6	c.382+1901G>A		intron_variant	Intron 2 of 2	5		ENSP00000355753.5

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15245 AN: 152058 Hom.: 1256 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.100 AC: 15270 AN: 152176 Hom.: 1258 Cov.: 33 AF XY: 0.100 AC XY: 7456 AN XY: 74404

African (AFR) AF: 0.225 AC: 9345 AN: 41470

American (AMR) AF: 0.0493 AC: 754 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3470

East Asian (EAS) AF: 0.0778 AC: 404 AN: 5190

South Asian (SAS) AF: 0.152 AC: 732 AN: 4824

European-Finnish (FIN) AF: 0.0529 AC: 561 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0462 AC: 3144 AN: 68010

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0804 Hom.: 108

Bravo AF: 0.105

Asia WGS AF: 0.138 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.20
PhyloP100		-2.1
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: rs708755; hg19: chr1-226786583;