16-87428363-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.508
Variant links:
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]

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ACMG classification

Classification made for transcript

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
ZCCHC14NM_015144.3 linkc.769-4482C>G intron_variant Intron 3 of 12 ENST00000671377.2 NP_055959.2 Q8WYQ9
ZCCHC14XM_005255858.4 linkc.769-4482C>G intron_variant Intron 3 of 11 XP_005255915.3 Q8WYQ9
ZCCHC14XM_017023082.3 linkc.250-4482C>G intron_variant Intron 3 of 11 XP_016878571.1
ZCCHC14XR_243401.4 linkn.1555-4482C>G intron_variant Intron 3 of 13

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZCCHC14ENST00000671377.2 linkc.769-4482C>G intron_variant Intron 3 of 12 NM_015144.3 ENSP00000499622.1 A0A590UJW6
ZCCHC14ENST00000268616.9 linkc.358-4482C>G intron_variant Intron 3 of 12 1 ENSP00000268616.4 Q8WYQ9-1
ZCCHC14ENST00000568020.6 linkn.388-4482C>G intron_variant Intron 3 of 13 1 ENSP00000455431.2 A0A5F9XIK1
ZCCHC14ENST00000561928.1 linkc.7-4482C>G intron_variant Intron 1 of 9 5 ENSP00000456499.1 H3BS18

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9646303; hg19: chr16-87461969; API