chr4-25362237-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024936.3(ZCCHC4):c.1145C>T(p.Pro382Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 1,610,652 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P382R) has been classified as Uncertain significance.
Frequency
Consequence
NM_024936.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZCCHC4 | NM_024936.3 | c.1145C>T | p.Pro382Leu | missense_variant | 10/13 | ENST00000302874.9 | |
ZCCHC4 | XM_011513835.3 | c.1190C>T | p.Pro397Leu | missense_variant | 11/14 | ||
ZCCHC4 | XM_017008129.3 | c.893C>T | p.Pro298Leu | missense_variant | 8/11 | ||
ZCCHC4 | XR_925324.4 | n.1226C>T | non_coding_transcript_exon_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZCCHC4 | ENST00000302874.9 | c.1145C>T | p.Pro382Leu | missense_variant | 10/13 | 1 | NM_024936.3 | P1 | |
ZCCHC4 | ENST00000507760.5 | c.*130C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 1 | ||||
ZCCHC4 | ENST00000505412.1 | c.740C>T | p.Pro247Leu | missense_variant | 7/10 | 3 | |||
ZCCHC4 | ENST00000508058.1 | n.284C>T | non_coding_transcript_exon_variant | 2/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0171 AC: 2603AN: 152094Hom.: 75 Cov.: 33
GnomAD3 exomes AF: 0.00561 AC: 1393AN: 248390Hom.: 32 AF XY: 0.00479 AC XY: 646AN XY: 134838
GnomAD4 exome AF: 0.00251 AC: 3664AN: 1458440Hom.: 82 Cov.: 29 AF XY: 0.00232 AC XY: 1683AN XY: 725596
GnomAD4 genome AF: 0.0172 AC: 2612AN: 152212Hom.: 75 Cov.: 33 AF XY: 0.0168 AC XY: 1254AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at