chr16-87411704-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015144.3(ZCCHC14):c.3017C>T(p.Thr1006Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015144.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZCCHC14 | NM_015144.3 | c.3017C>T | p.Thr1006Met | missense_variant | 12/13 | ENST00000671377.2 | |
ZCCHC14 | XM_005255858.4 | c.3017C>T | p.Thr1006Met | missense_variant | 12/12 | ||
ZCCHC14 | XM_017023082.3 | c.2498C>T | p.Thr833Met | missense_variant | 12/12 | ||
ZCCHC14 | XR_243401.4 | n.3803C>T | non_coding_transcript_exon_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZCCHC14 | ENST00000671377.2 | c.3017C>T | p.Thr1006Met | missense_variant | 12/13 | NM_015144.3 | P1 | ||
ZCCHC14 | ENST00000268616.9 | c.2606C>T | p.Thr869Met | missense_variant | 12/13 | 1 | |||
ZCCHC14 | ENST00000568020.6 | c.2639C>T | p.Thr880Met | missense_variant, NMD_transcript_variant | 12/14 | 1 | |||
ZCCHC14 | ENST00000561928.1 | c.2258C>T | p.Thr753Met | missense_variant | 10/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251208Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135844
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461768Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727188
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.2606C>T (p.T869M) alteration is located in exon 12 (coding exon 12) of the ZCCHC14 gene. This alteration results from a C to T substitution at nucleotide position 2606, causing the threonine (T) at amino acid position 869 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at