19-32352841-G-A

Variant names:

• chr19-32352841-G-A
• NM_001136156.2:c.11G>A

Variant summary

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

The NM_001136156.2(ZNF507):​c.11G>A​(p.Ser4Asn) 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF507 NM_001136156.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.11
• Publications: 0 publications found

Genes affected

ZNF507 (HGNC:23783): (zinc finger protein 507) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DPY19L3-DT (HGNC:55307): (DPY19L3 divergent transcript)

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=0.118652076).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136156.2. 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
	ZNF507	NM_001136156.2	MANE Select	c.11G>A	p.Ser4Asn	missense	Exon 3 of 7	NP_001129628.1	Q8TCN5-1
	ZNF507	NM_014910.5		c.11G>A	p.Ser4Asn	missense	Exon 2 of 6	NP_055725.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF507	ENST00000355898.6	TSL:1 MANE Select	c.11G>A	p.Ser4Asn	missense	Exon 3 of 7	ENSP00000348162.4	Q8TCN5-1
	ZNF507	ENST00000544431.5	TSL:1	c.11G>A	p.Ser4Asn	missense	Exon 3 of 8	ENSP00000441549.1	B9EGE7
	ZNF507	ENST00000311921.8	TSL:1	c.11G>A	p.Ser4Asn	missense	Exon 2 of 6	ENSP00000312277.2	Q8TCN5-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

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	0.095
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	18
DANN	Benign	0.96
DEOGEN2	Benign	0.024	T
Eigen	Benign	0.0045
Eigen_PC	Benign	0.11
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.67	T
M_CAP	Benign	0.0061	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.9	L
PhyloP100		3.1
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.26	N
REVEL	Benign	0.074
Sift	Benign	0.046	D
Sift4G	Benign	0.18	T
Polyphen		0.18	B
Vest4		0.13
MutPred		0.16		Loss of phosphorylation at S4 (P = 0.0149)
MVP		0.39
MPC		0.054
ClinPred		0.32	T
GERP RS		3.2
Varity_R		0.17
gMVP		0.26
Mutation Taster		=95/5	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: chr19-32843747;