ZNF396 p.His211His

Variant names:

• chr18-35369589-A-A
• NM_001322286.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr18-35369590--
• chr18-35369590-A-G

Variant summary

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

The NM_001322286.2(ZNF396):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF396 NM_001322286.2 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 0 publications found

Genes affected

ZNF396 (HGNC:18824): (zinc finger protein 396) Enables protein heterodimerization activity; protein homodimerization activity; and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription, DNA-templated. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322286.2. 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
	ZNF396	NM_001322286.2	MANE Select	c.		exon_region	Exon 4 of 4	NP_001309215.1	Q96N95-1
	ZNF396	NM_001322290.2		c.		exon_region	Exon 5 of 5	NP_001309219.1	Q96N95-1
	ZNF396	NM_145756.3		c.		exon_region	Exon 4 of 5	NP_665699.1	Q96N95-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF396	ENST00000589332.7	TSL:1 MANE Select	c.		exon_region	Exon 4 of 4	ENSP00000466500.1	Q96N95-1
	ZNF396	ENST00000306346.5	TSL:1	c.		exon_region	Exon 4 of 5	ENSP00000302310.1	Q96N95-3
	ZNF396	ENST00000862521.1		c.		exon_region	Exon 5 of 5	ENSP00000532580.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr18-32949553;