rs10509559

Variant names:

• chr10-88908227-A-G
• rs10509559
• NM_020799.4:c.249-475A>G

Variant summary

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

The NM_020799.4(STAMBPL1):​c.249-475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,196 control chromosomes in the GnomAD database, including 570 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 (570 hom., cov: 32)
• Consequence: STAMBPL1 NM_020799.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• 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=-0.84).
• 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.249-475A>G		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.249-475A>G		intron_variant	Intron 3 of 10	1	NM_020799.4	ENSP00000360994.3
STAMBPL1	ENST00000371924.5	c.249-475A>G		intron_variant	Intron 2 of 9	1		ENSP00000360992.1
STAMBPL1	ENST00000371927.7	c.249-475A>G		intron_variant	Intron 3 of 10	2		ENSP00000360995.3

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8195 AN: 152078 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00961

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00587

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0539 AC: 8210 AN: 152196 Hom.: 570 Cov.: 32 AF XY: 0.0532 AC XY: 3956 AN XY: 74416

African (AFR) AF: 0.157 AC: 6533 AN: 41498

American (AMR) AF: 0.0211 AC: 322 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3472

East Asian (EAS) AF: 0.112 AC: 581 AN: 5182

South Asian (SAS) AF: 0.0297 AC: 143 AN: 4820

European-Finnish (FIN) AF: 0.00961 AC: 102 AN: 10612

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

European-Non Finnish (NFE) AF: 0.00587 AC: 399 AN: 68008

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0337 Hom.: 41

Bravo AF: 0.0603

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.28
DANN	Benign	0.51
PhyloP100		-0.42
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: rs10509559; hg19: chr10-90667984;