12-14424942-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018179.5(ATF7IP):c.1027A>G(p.Asn343Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,454,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.1027A>G | p.Asn343Asp | missense_variant | 2/15 | ENST00000261168.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATF7IP | ENST00000261168.9 | c.1027A>G | p.Asn343Asp | missense_variant | 2/15 | 5 | NM_018179.5 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152218Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000247 AC: 6AN: 243328Hom.: 0 AF XY: 0.0000304 AC XY: 4AN XY: 131738
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1454524Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 723370
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.1027A>G (p.N343D) alteration is located in exon 2 (coding exon 1) of the ATF7IP gene. This alteration results from a A to G substitution at nucleotide position 1027, causing the asparagine (N) at amino acid position 343 to be replaced by an aspartic acid (D). 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