chr1-226586341-T-C

Variant names:

• chr1-226586341-T-C
• rs865682
• NM_001003665.4:c.203-10461T>C

Variant summary

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

The NM_001003665.4(STUM):​c.203-10461T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,238 control chromosomes in the GnomAD database, including 66,262 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 0.93 (66262 hom., cov: 31)
• Consequence: STUM NM_001003665.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STUM	NM_001003665.4	c.203-10461T>C		intron_variant	Intron 1 of 3	ENST00000366788.8	NP_001003665.1
STUM	NM_001410930.1	c.203-10461T>C		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.203-10461T>C		intron_variant	Intron 1 of 3	5	NM_001003665.4	ENSP00000355752.3
STUM	ENST00000366789.6	c.203-10461T>C		intron_variant	Intron 1 of 2	5		ENSP00000355753.5

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141805 AN: 152120 Hom.: 66196 Cov.: 31

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.932 AC: 141931 AN: 152238 Hom.: 66262 Cov.: 31 AF XY: 0.935 AC XY: 69628 AN XY: 74438

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.927

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.940

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.922

Alfa AF: 0.902 Hom.: 74306

Bravo AF: 0.932

Asia WGS AF: 0.964 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.22

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: rs865682; hg19: chr1-226774042;