ZC3H7A p.Val787Val

Variant names:

• chr16-11758497-C-C
• NM_014153.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr16-11758498--
• chr16-11758498-A-G
• chr16-11758498-A-T
• chr16-11758498-A-C

Variant summary

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

The NM_014153.4(ZC3H7A):​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: ZC3H7A NM_014153.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 0 publications found

Genes affected

ZC3H7A (HGNC:30959): (zinc finger CCCH-type containing 7A) Enables miRNA binding activity. Involved in production of miRNAs involved in gene silencing by miRNA. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TXNDC11-AS1 (HGNC:56375): (TXNDC11 antisense RNA 1)

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_014153.4. 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
	ZC3H7A	NM_014153.4	MANE Select	c.		exon_region	Exon 20 of 23	NP_054872.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZC3H7A	ENST00000355758.9	TSL:1 MANE Select	c.		exon_region	Exon 20 of 23	ENSP00000347999.4	Q8IWR0-1
	ZC3H7A	ENST00000396516.6	TSL:1	c.		exon_region	Exon 19 of 22	ENSP00000379773.2	Q8IWR0-1
	ZC3H7A	ENST00000575984.1	TSL:1	c.		exon_region	Exon 1 of 4	ENSP00000459477.1	Q8IWR0-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7

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: chr16-11852353;