rs12378217

Variant names:

• chr9-37331608-T-C
• rs12378217
• NM_032226.3:c.987+3774T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-37331608-T-C
• chr9-37331608-T-G

Variant summary

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

The NM_032226.3(ZCCHC7):​c.987+3774T>C variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZCCHC7 NM_032226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 2 publications found

Genes affected

ZCCHC7 (HGNC:26209): (zinc finger CCHC-type containing 7) Enables RNA binding activity. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032226.3. 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
	ZCCHC7	NM_032226.3	MANE Select	c.987+3774T>C		intron	N/A	NP_115602.2	Q8N3Z6-1
	ZCCHC7	NM_001289119.2		c.987+3774T>C		intron	N/A	NP_001276048.1	Q8N3Z6-1
	ZCCHC7	NM_001289120.2		c.987+3774T>C		intron	N/A	NP_001276049.1	Q8N3Z6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZCCHC7	ENST00000336755.10	TSL:2 MANE Select	c.987+3774T>C		intron	N/A	ENSP00000337839.5	Q8N3Z6-1
	ZCCHC7	ENST00000534928.5	TSL:1	c.987+3774T>C		intron	N/A	ENSP00000443113.2	Q8N3Z6-1
	ZCCHC7	ENST00000461038.5	TSL:1	n.1267+3774T>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		0.33

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: rs12378217; hg19: chr9-37331605;