rs10509558

Variant names:

• chr10-88906276-G-A
• rs10509558
• NM_020799.4:c.248+616G>A

Variant summary

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

The NM_020799.4(STAMBPL1):​c.248+616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,296 control chromosomes in the GnomAD database, including 571 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 0.054 (571 hom., cov: 32)
• Consequence: STAMBPL1 NM_020799.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 1 publications found

Genes affected

STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAMBPL1	NM_020799.4	c.248+616G>A		intron_variant	Intron 3 of 10	ENST00000371926.8	NP_065850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAMBPL1	ENST00000371926.8	c.248+616G>A		intron_variant	Intron 3 of 10	1	NM_020799.4	ENSP00000360994.3
STAMBPL1	ENST00000371924.5	c.248+616G>A		intron_variant	Intron 2 of 9	1		ENSP00000360992.1
STAMBPL1	ENST00000371927.7	c.248+616G>A		intron_variant	Intron 3 of 10	2		ENSP00000360995.3

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8203 AN: 152178 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.00961

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0540 AC: 8218 AN: 152296 Hom.: 571 Cov.: 32 AF XY: 0.0532 AC XY: 3963 AN XY: 74480

African (AFR) AF: 0.157 AC: 6541 AN: 41548

American (AMR) AF: 0.0210 AC: 321 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3470

East Asian (EAS) AF: 0.112 AC: 579 AN: 5188

South Asian (SAS) AF: 0.0301 AC: 145 AN: 4824

European-Finnish (FIN) AF: 0.00961 AC: 102 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00588 AC: 400 AN: 68026

Other (OTH) AF: 0.0474 AC: 100 AN: 2110

Alfa AF: 0.0398 Hom.: 58

Bravo AF: 0.0603

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.0
DANN	Benign	0.15
PhyloP100		0.43
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: rs10509558; hg19: chr10-90666033;