rs142629776

Variant names:

• chr10-88914618-T-A
• rs142629776
• NM_020799.4:c.863T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-88914618-T-A
• chr10-88914618-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020799.4(STAMBPL1):​c.863T>A​(p.Val288Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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)
• Consequence: STAMBPL1 NM_020799.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.71

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22177076).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAMBPL1	NM_020799.4	c.863T>A	p.Val288Glu	missense_variant	Exon 7 of 11	ENST00000371926.8	NP_065850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAMBPL1	ENST00000371926.8	c.863T>A	p.Val288Glu	missense_variant	Exon 7 of 11	1	NM_020799.4	ENSP00000360994.3
STAMBPL1	ENST00000371924.5	c.863T>A	p.Val288Glu	missense_variant	Exon 6 of 10	1		ENSP00000360992.1
STAMBPL1	ENST00000371927.7	c.863T>A	p.Val288Glu	missense_variant	Exon 7 of 11	2		ENSP00000360995.3
STAMBPL1	ENST00000371922.1	n.1188T>A		non_coding_transcript_exon_variant	Exon 2 of 6	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Benign	0.95
DEOGEN2	Benign	0.0026	T;.;T;.
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.12
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Uncertain	0.90	D;D;.;D
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.22	T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.47	N;N;N;.
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.71	N;N;N;N
REVEL	Benign	0.12
Sift	Benign	0.54	T;T;T;T
Sift4G	Benign	1.0	T;T;T;T
Polyphen		0.0040	B;B;B;.
Vest4		0.52
MutPred		0.37		Gain of disorder (P = 0.0025);Gain of disorder (P = 0.0025);Gain of disorder (P = 0.0025);.;
MVP		0.60
MPC		0.14
ClinPred		0.33	T
GERP RS		5.7
Varity_R		0.41
gMVP		0.59

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: rs142629776; hg19: chr10-90674375;