NM_007157.4:c.203G>A

Variant names:

• chrX-57592251-G-A
• rs2057894739
• NM_007157.4:c.203G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_007157.4(ZXDB):​c.203G>A​(p.Gly68Asp) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: ZXDB NM_007157.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.19
• Publications: 0 publications found

Genes affected

ZXDB (HGNC:13199): (zinc finger X-linked duplicated B) The ZXDB gene is one of a pair of duplicated zinc finger genes on chromosome Xp11.21 (Greig et al., 1993 [PubMed 8268913]); see also ZXDA (MIM 300235).[supplied by OMIM, Jul 2010]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14503643).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007157.4. 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
	ZXDB	NM_007157.4	MANE Select	c.203G>A	p.Gly68Asp	missense	Exon 1 of 1	NP_009088.1	P98169

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZXDB	ENST00000374888.3	TSL:6 MANE Select	c.203G>A	p.Gly68Asp	missense	Exon 1 of 1	ENSP00000364023.1	P98169

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1051750 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 340942

African (AFR) AF: 0.00 AC: 0 AN: 22853

American (AMR) AF: 0.00 AC: 0 AN: 30755

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18072

East Asian (EAS) AF: 0.00 AC: 0 AN: 25881

South Asian (SAS) AF: 0.00 AC: 0 AN: 49931

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32648

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2793

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 824655

Other (OTH) AF: 0.00 AC: 0 AN: 44162

GnomAD4 genome Cov.: 23

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	0.089
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.96
DEOGEN2	Benign	0.0063	T
FATHMM_MKL	Benign	0.25	N
LIST_S2	Benign	0.35	T
M_CAP	Pathogenic	0.48	D
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		1.2
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	0.30	N
REVEL	Benign	0.065
Sift	Benign	0.11	T
Sift4G	Uncertain	0.014	D
Polyphen		0.0	B
Vest4		0.065
MutPred		0.16		Loss of methylation at R67 (P = 0.0371)
MVP		0.12
MPC		1.4
ClinPred		0.037	T
GERP RS		1.4
PromoterAI		0.20	Neutral
Varity_R		0.10
gMVP		0.094
Mutation Taster		=96/4	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: rs2057894739; hg19: chrX-57618684;