10-88913183-G-T

Variant names:

• chr10-88913183-G-T
• NM_020799.4:c.503G>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_020799.4(STAMBPL1):​c.503G>T​(p.Arg168Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,480 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: STAMBPL1 NM_020799.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.60

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

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31432322).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAMBPL1	NM_020799.4	c.503G>T	p.Arg168Leu	missense_variant	Exon 6 of 11	ENST00000371926.8	NP_065850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAMBPL1	ENST00000371926.8	c.503G>T	p.Arg168Leu	missense_variant	Exon 6 of 11	1	NM_020799.4	ENSP00000360994.3
STAMBPL1	ENST00000371924.5	c.503G>T	p.Arg168Leu	missense_variant	Exon 5 of 10	1		ENSP00000360992.1
STAMBPL1	ENST00000371927.7	c.503G>T	p.Arg168Leu	missense_variant	Exon 6 of 11	2		ENSP00000360995.3
STAMBPL1	ENST00000371922.1	n.828G>T		non_coding_transcript_exon_variant	Exon 1 of 6	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461480 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 727032

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.30
CADD	Pathogenic	31
DANN	Uncertain	1.0
DEOGEN2	Benign	0.087	T;.;T;.
Eigen	Uncertain	0.65
Eigen_PC	Pathogenic	0.69
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.87	D;D;.;D
M_CAP	Benign	0.022	T
MetaRNN	Benign	0.31	T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Uncertain	2.2	M;M;M;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-3.4	D;D;D;D
REVEL	Benign	0.17
Sift	Uncertain	0.011	D;D;D;D
Sift4G	Benign	0.085	T;T;T;T
Polyphen		1.0	D;P;D;.
Vest4		0.58
MutPred		0.32		Loss of MoRF binding (P = 0.0442);Loss of MoRF binding (P = 0.0442);Loss of MoRF binding (P = 0.0442);.;
MVP		0.43
MPC		0.46
ClinPred		0.92	D
GERP RS		6.0
Varity_R		0.35
gMVP		0.54

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-90672940;