rs151344611

Positions:

• chr7-151180977-G-A
• chr7-151180977-G-C

Variant summary

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

The NM_001142459.2(ASB10):​c.1066C>T​(p.His356Tyr) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ASB10 NM_001142459.2 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.88

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19608837).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASB10	NM_001142459.2	c.1066C>T	p.His356Tyr	missense_variant	3/6	ENST00000420175.3	NP_001135931.2
ASB10	NM_080871.4	c.1021C>T	p.His341Tyr	missense_variant	3/6		NP_543147.2
ASB10	NM_001142460.1	c.1066C>T	p.His356Tyr	missense_variant	3/5		NP_001135932.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASB10	ENST00000420175.3	c.1066C>T	p.His356Tyr	missense_variant	3/6	1	NM_001142459.2	ENSP00000391137	P4
ASB10	ENST00000275838.5	c.1066C>T	p.His356Tyr	missense_variant	3/5	1		ENSP00000275838
ASB10	ENST00000377867.7	c.1021C>T	p.His341Tyr	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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.096	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Benign	0.96
DEOGEN2	Benign	0.019	.;.;T
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.20
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Benign	0.80	T;T;T
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.20	T;T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	0.86	L;.;L
MutationTaster	Benign	0.87	D;D;D;D;D
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-1.9	N;N;N
REVEL	Benign	0.058
Sift	Benign	0.24	T;T;T
Sift4G	Benign	0.43	T;T;T
Polyphen		0.057, 0.019	.;B;B
Vest4		0.28
MVP		0.60
MPC		0.060
ClinPred		0.25	T
GERP RS		4.2
Varity_R		0.087
gMVP		0.49

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: rs151344611; hg19: chr7-150878064;