X-57120448-C-G

Variant names:

• chrX-57120448-C-G
• NM_001006681.2:c.182G>C

Variant summary

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

The NM_001006681.2(SPIN2B):​c.182G>C​(p.Gly61Ala) variant causes a missense change. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 7)
  • Exomes 𝑓: 0.0000013 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: SPIN2B NM_001006681.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.86
• Publications: 0 publications found

Genes affected

SPIN2B (HGNC:33147): (spindlin family member 2B) Enables methylated histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006681.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPIN2B	NM_001006681.2	MANE Select	c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	NP_001006682.1	Q9BPZ2
	SPIN2B	NM_001006682.2		c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	NP_001006683.1	Q9BPZ2
	SPIN2B	NM_001006683.2		c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	NP_001006684.1	Q9BPZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPIN2B	ENST00000434397.3	TSL:1 MANE Select	c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	ENSP00000404314.2	Q9BPZ2
	SPIN2B	ENST00000275988.5	TSL:1	c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	ENSP00000275988.5	Q9BPZ2
	SPIN2B	ENST00000333933.3	TSL:1	c.182G>C	p.Gly61Ala	missense	Exon 2 of 2	ENSP00000335008.3	Q9BPZ2

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000133 AC: 1 AN: 754075 Hom.: 0 Cov.: 12 AF XY: 0.00000514 AC XY: 1 AN XY: 194649

African (AFR) AF: 0.00 AC: 0 AN: 19626

American (AMR) AF: 0.00 AC: 0 AN: 28708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14941

East Asian (EAS) AF: 0.00 AC: 0 AN: 27953

South Asian (SAS) AF: 0.00 AC: 0 AN: 40026

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34780

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2366

European-Non Finnish (NFE) AF: 0.00000181 AC: 1 AN: 551344

Other (OTH) AF: 0.00 AC: 0 AN: 34331

GnomAD4 genome Cov.: 7

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.031	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	18
DANN	Benign	0.93
DEOGEN2	Benign	0.16	T
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.021	T
MetaRNN	Uncertain	0.67	D
MetaSVM	Benign	-0.74	T
MutationAssessor	Benign	1.6	L
PhyloP100		3.9
PrimateAI	Pathogenic	0.89	D
PROVEAN	Uncertain	-4.2	D
REVEL	Benign	0.27
Sift	Benign	0.085	T
Sift4G	Uncertain	0.0080	D
Polyphen		0.0020	B
Vest4		0.26
MutPred		0.60		Gain of ubiquitination at K59 (P = 0.0846)
MVP		0.79
MPC		2.1
ClinPred		0.83	D
GERP RS		2.4
PromoterAI		-0.017	Neutral
Varity_R		0.51
gMVP		0.65
Mutation Taster		=56/44	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

hg19: chrX-57146881;