chr9-37331608-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032226.3(ZCCHC7):​c.987+3774T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,582 control chromosomes in the GnomAD database, including 1,747 homozygotes. 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: 𝑓 0.14 (1747 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZCCHC7	NM_032226.3	c.987+3774T>G		intron_variant	Intron 6 of 8	ENST00000336755.10	NP_115602.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZCCHC7	ENST00000336755.10	c.987+3774T>G		intron_variant	Intron 6 of 8	2	NM_032226.3	ENSP00000337839.5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21317 AN: 151464 Hom.: 1745 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.141 AC: 21317 AN: 151582 Hom.: 1747 Cov.: 32 AF XY: 0.144 AC XY: 10657 AN XY: 74062

African (AFR) AF: 0.0710 AC: 2946 AN: 41484

American (AMR) AF: 0.149 AC: 2263 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3462

East Asian (EAS) AF: 0.0998 AC: 515 AN: 5160

South Asian (SAS) AF: 0.135 AC: 652 AN: 4816

European-Finnish (FIN) AF: 0.244 AC: 2578 AN: 10580

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11516 AN: 67574

Other (OTH) AF: 0.137 AC: 289 AN: 2106

Alfa AF: 0.160 Hom.: 742

Bravo AF: 0.130

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

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;