rs1051041

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-124834597-G-A
• chr10-124834597-G-T

Variant summary

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

The NM_032182.4(ABRAXAS2):​c.874G>A​(p.Gly292Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: ABRAXAS2 NM_032182.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.91

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

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=0.25829536).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABRAXAS2	NM_032182.4	c.874G>A	p.Gly292Ser	missense_variant	Exon 9 of 9	ENST00000298492.6	NP_115558.3
ABRAXAS2	XM_047424888.1	c.562G>A	p.Gly188Ser	missense_variant	Exon 8 of 8		XP_047280844.1
ABRAXAS2	XM_047424889.1	c.562G>A	p.Gly188Ser	missense_variant	Exon 6 of 6		XP_047280845.1
ABRAXAS2	XM_047424891.1	c.562G>A	p.Gly188Ser	missense_variant	Exon 6 of 6		XP_047280847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABRAXAS2	ENST00000298492.6	c.874G>A	p.Gly292Ser	missense_variant	Exon 9 of 9	1	NM_032182.4	ENSP00000298492.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.048	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.045	T
Eigen	Uncertain	0.32
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.82	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.26	T
MetaSVM	Benign	-0.98	T
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.18
Sift	Uncertain	0.017	D
Sift4G	Benign	0.25	T
Polyphen		1.0	D
Vest4		0.36
MutPred		0.24		Loss of helix (P = 0.0041);
MVP		0.71
MPC		0.56
ClinPred		0.77	D
GERP RS		5.3
Varity_R		0.098
gMVP		0.22

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: chr10-126523166;