NM_032182.4:c.874G>T

Variant names:

• chr10-124834597-G-T
• rs1051041
• NM_032182.4:c.874G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032182.4(ABRAXAS2):​c.874G>T​(p.Gly292Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ABRAXAS2 NM_032182.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.91
• Publications: 1 publications found

Genes affected

ABRAXAS2 (HGNC:28975): (abraxas 2, BRISC complex subunit) Enables microtubule binding activity and polyubiquitin modification-dependent protein binding activity. Involved in several processes, including mitotic spindle assembly; protein K63-linked deubiquitination; and response to ischemia. Located in cytoplasm. Part of BRISC complex. Colocalizes with microtubule minus-end; midbody; and spindle pole centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032182.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABRAXAS2	NM_032182.4	MANE Select	c.874G>T	p.Gly292Cys	missense	Exon 9 of 9	NP_115558.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABRAXAS2	ENST00000298492.6	TSL:1 MANE Select	c.874G>T	p.Gly292Cys	missense	Exon 9 of 9	ENSP00000298492.5
	ABRAXAS2	ENST00000899981.1		c.1279G>T	p.Gly427Cys	missense	Exon 9 of 9	ENSP00000570040.1
	ABRAXAS2	ENST00000899980.1		c.766G>T	p.Gly256Cys	missense	Exon 7 of 7	ENSP00000570039.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.058	T
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.031	T
Eigen	Uncertain	0.46
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.76	T
M_CAP	Benign	0.025	T
MetaRNN	Uncertain	0.43	T
MetaSVM	Benign	-0.73	T
PhyloP100		4.9
PrimateAI	Uncertain	0.60	T
PROVEAN	Benign	0.63	N
REVEL	Benign	0.17
Sift	Benign	0.049	D
Sift4G	Uncertain	0.042	D
Polyphen		1.0	D
Vest4		0.52
MutPred		0.23		Loss of methylation at R293 (P = 0.0891)
MVP		0.60
MPC		1.1
ClinPred		0.78	D
GERP RS		5.3
Varity_R		0.14
gMVP		0.22
Mutation Taster		=68/32	polymorphism

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: rs1051041; hg19: chr10-126523166;