chr12-14424300-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018179.5(ATF7IP):c.385C>G(p.Pro129Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,614,116 control chromosomes in the GnomAD database, including 1 homozygotes. 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_018179.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATF7IP | NM_018179.5 | c.385C>G | p.Pro129Ala | missense_variant | 2/15 | ENST00000261168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATF7IP | ENST00000261168.9 | c.385C>G | p.Pro129Ala | missense_variant | 2/15 | 5 | NM_018179.5 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152222Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 250588Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135792
GnomAD4 exome AF: 0.000116 AC: 170AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.000117 AC XY: 85AN XY: 727248
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152222Hom.: 1 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2021 | The c.385C>G (p.P129A) alteration is located in exon 2 (coding exon 1) of the ATF7IP gene. This alteration results from a C to G substitution at nucleotide position 385, causing the proline (P) at amino acid position 129 to be replaced by an alanine (A). 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