chr1-37475795-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_025079.3(ZC3H12A):c.299C>T(p.Pro100Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,612,496 control chromosomes in the GnomAD database, including 21 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 (★).
Frequency
Consequence
NM_025079.3 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 |
---|---|---|---|---|---|---|---|
ZC3H12A | NM_025079.3 | c.299C>T | p.Pro100Leu | missense_variant | 2/6 | ENST00000373087.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H12A | ENST00000373087.7 | c.299C>T | p.Pro100Leu | missense_variant | 2/6 | 1 | NM_025079.3 | P1 | |
ZC3H12A | ENST00000640233.1 | c.299C>T | p.Pro100Leu | missense_variant, NMD_transcript_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00530 AC: 806AN: 152184Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00179 AC: 445AN: 248784Hom.: 1 AF XY: 0.00130 AC XY: 176AN XY: 134872
GnomAD4 exome AF: 0.000641 AC: 936AN: 1460194Hom.: 12 Cov.: 31 AF XY: 0.000536 AC XY: 389AN XY: 726194
GnomAD4 genome ? AF: 0.00531 AC: 808AN: 152302Hom.: 9 Cov.: 33 AF XY: 0.00513 AC XY: 382AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at