rs9646303

Variant names:

• chr16-87428363-G-A
• rs9646303
• NM_015144.3:c.769-4482C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-87428363-G-A
• chr16-87428363-G-C

Variant summary

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

The NM_015144.3(ZCCHC14):​c.769-4482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,174 control chromosomes in the GnomAD database, including 53,807 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 0.84 (53807 hom., cov: 32)
• Consequence: ZCCHC14 NM_015144.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 18 publications found

Genes affected

ZCCHC14 (HGNC:24134): (zinc finger CCHC-type containing 14) Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015144.3. 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
	ZCCHC14	NM_015144.3	MANE Select	c.769-4482C>T		intron	N/A	NP_055959.2	A0A590UJW6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZCCHC14	ENST00000671377.2	MANE Select	c.769-4482C>T		intron	N/A	ENSP00000499622.1	A0A590UJW6
	ZCCHC14	ENST00000268616.9	TSL:1	c.358-4482C>T		intron	N/A	ENSP00000268616.4	Q8WYQ9-1
	ZCCHC14	ENST00000568020.6	TSL:1	n.388-4482C>T		intron	N/A	ENSP00000455431.2	A0A5F9XIK1

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127312 AN: 152056 Hom.: 53762 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.837 AC: 127408 AN: 152174 Hom.: 53807 Cov.: 32 AF XY: 0.829 AC XY: 61723 AN XY: 74414

African (AFR) AF: 0.860 AC: 35693 AN: 41522

American (AMR) AF: 0.711 AC: 10859 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2778 AN: 5162

South Asian (SAS) AF: 0.838 AC: 4043 AN: 4822

European-Finnish (FIN) AF: 0.855 AC: 9053 AN: 10592

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59362 AN: 68020

Other (OTH) AF: 0.821 AC: 1735 AN: 2112

Alfa AF: 0.851 Hom.: 165315

Bravo AF: 0.820

Asia WGS AF: 0.725 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.68
PhyloP100		-0.51
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: rs9646303; hg19: chr16-87461969;