X-135287762-G-A

Variant names:

• chrX-135287762-G-A
• NM_007131.5:c.908C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_007131.5(ZNF75D):​c.908C>T​(p.Ser303Leu) 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 Likely benign (★).

• Frequency: Genomes: not found (cov: 24)
• Consequence: ZNF75D NM_007131.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.573
• Publications: 0 publications found

Genes affected

ZNF75D (HGNC:13145): (zinc finger protein 75D) This gene encodes a protein that likely functions as a transcription factor. The protein, which belongs to the ZNF75 family, includes an N-terminal SCAN domain, a KRAB box, and five C2H2-type zinc finger motifs. Another functional gene belonging to this family is located on chromosome 16, while pseudogenes have been identified on chromosomes 11 and 12. Alternative splicing results in multiple transcripts variants. [provided by RefSeq, Jun 2010]

ETDC (HGNC:53450): (embryonic testis differentiation homolog C)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06584713).
• BP6: Variant X-135287762-G-A is Benign according to our data. Variant chrX-135287762-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3478218.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007131.5. 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
	ZNF75D	NM_007131.5	MANE Select	c.908C>T	p.Ser303Leu	missense	Exon 7 of 7	NP_009062.2
	ZNF75D	NM_001185063.2		c.623C>T	p.Ser208Leu	missense	Exon 4 of 4	NP_001171992.1	P51815-2
	ZNF75D	NR_110381.2		n.850-31985C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF75D	ENST00000370766.8	TSL:1 MANE Select	c.908C>T	p.Ser303Leu	missense	Exon 7 of 7	ENSP00000359802.3	P51815-1
	ZNF75D	ENST00000469456.1	TSL:1	n.680C>T		non_coding_transcript_exon	Exon 2 of 2
	ZNF75D	ENST00000865785.1		c.908C>T	p.Ser303Leu	missense	Exon 7 of 7	ENSP00000535844.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

ClinVar submissions

Significance: Likely benign

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	0.097
BayesDel_addAF	Benign	-0.52	T
BayesDel_noAF	Benign	-0.98
CADD	Benign	11
DANN	Benign	0.87
DEOGEN2	Benign	0.19	T
FATHMM_MKL	Benign	0.0013	N
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.066	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.66	N
PhyloP100		0.57
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-2.9	D
REVEL	Benign	0.018
Sift	Benign	0.72	T
Sift4G	Benign	0.45	T
Polyphen		0.0010	B
Vest4		0.045
MutPred		0.37		Gain of helix (P = 0.0225)
MVP		0.29
MPC		0.33
ClinPred		0.084	T
GERP RS		2.0
Varity_R		0.068
gMVP		0.21
Mutation Taster		=98/2	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-134421694;