16-87428363-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015144.3(ZCCHC14):​c.769-4482C>G 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: ZCCHC14 NM_015144.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZCCHC14	NM_015144.3	c.769-4482C>G		intron_variant	Intron 3 of 12	ENST00000671377.2	NP_055959.2
ZCCHC14	XM_005255858.4	c.769-4482C>G		intron_variant	Intron 3 of 11		XP_005255915.3
ZCCHC14	XM_017023082.3	c.250-4482C>G		intron_variant	Intron 3 of 11		XP_016878571.1
ZCCHC14	XR_243401.4	n.1555-4482C>G		intron_variant	Intron 3 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZCCHC14	ENST00000671377.2	c.769-4482C>G		intron_variant	Intron 3 of 12		NM_015144.3	ENSP00000499622.1
ZCCHC14	ENST00000268616.9	c.358-4482C>G		intron_variant	Intron 3 of 12	1		ENSP00000268616.4
ZCCHC14	ENST00000568020.6	n.388-4482C>G		intron_variant	Intron 3 of 13	1		ENSP00000455431.2
ZCCHC14	ENST00000561928.1	c.7-4482C>G		intron_variant	Intron 1 of 9	5		ENSP00000456499.1

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs9646303; hg19: chr16-87461969;