chr2-64552636-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_203437.4(AFTPH):c.1162A>G(p.Arg388Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 1,614,212 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_203437.4 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 |
---|---|---|---|---|---|---|---|
AFTPH | NM_203437.4 | c.1162A>G | p.Arg388Gly | missense_variant | 2/10 | ENST00000409933.6 | |
LOC105374773 | XR_007086343.1 | n.5406-1372T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFTPH | ENST00000409933.6 | c.1162A>G | p.Arg388Gly | missense_variant | 2/10 | 1 | NM_203437.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152264Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251172Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135822
GnomAD4 exome AF: 0.000289 AC: 422AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.000293 AC XY: 213AN XY: 727210
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152382Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74522
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2021 | The c.1162A>G (p.R388G) alteration is located in exon 2 (coding exon 1) of the AFTPH gene. This alteration results from a A to G substitution at nucleotide position 1162, causing the arginine (R) at amino acid position 388 to be replaced by a glycine (G). 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