rs104886482

Positions:

• chr7-151181047-G-C

Variant summary

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

The ENST00000420175.3(ASB10):​c.996C>G​(p.His332Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ASB10 ENST00000420175.3 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.90

Genes affected

ASB10 (HGNC:17185): (ankyrin repeat and SOCS box containing 10) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. The SOCS box serves to couple suppressor of cytokine signaling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.996C>G	p.His332Gln	missense_variant	3/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4	c.951C>G	p.His317Gln	missense_variant	3/6		NP_543147.2
ASB10	NM_001142460.1	c.996C>G	p.His332Gln	missense_variant	3/5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3	c.996C>G	p.His332Gln	missense_variant	3/6	1	NM_001142459.2	ENSP00000391137	P4
ASB10	ENST00000275838.5	c.996C>G	p.His332Gln	missense_variant	3/5	1		ENSP00000275838
ASB10	ENST00000377867.7	c.951C>G	p.His317Gln	missense_variant	3/6	2		ENSP00000367098	A1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

Glaucoma 1, open angle, F Other:1

not provided, no classification provided

literature only

Casey Eye Institute Glaucoma Genetics Lab

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Uncertain	0.090
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.021	.;.;T
Eigen	Benign	0.058
Eigen_PC	Benign	0.012
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.75	T;T;T
M_CAP	Benign	0.036	D
MetaRNN	Uncertain	0.45	T;T;T
MetaSVM	Benign	-0.70	T
MutationAssessor	Benign	1.1	L;.;L
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-1.8	N;N;N
REVEL	Uncertain	0.47
Sift	Benign	0.12	T;T;T
Sift4G	Benign	0.15	T;T;T
Polyphen		1.0	.;D;D
Vest4		0.61
MVP		0.52
MPC		0.092
ClinPred		0.49	T
GERP RS		1.6
Varity_R		0.16
gMVP		0.60

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: rs104886482; hg19: chr7-150878134;