17-81545882-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025161.6(FAAP100):c.2174G>A(p.Gly725Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,605,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/24 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025161.6 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAAP100 | NM_025161.6 | c.2174G>A | p.Gly725Asp | missense_variant, splice_region_variant | Exon 6 of 9 | ENST00000327787.13 | NP_079437.5 | |
FAAP100 | XM_006722111.3 | c.1760G>A | p.Gly587Asp | missense_variant, splice_region_variant | Exon 6 of 9 | XP_006722174.1 | ||
FAAP100 | XM_047436848.1 | c.1721G>A | p.Gly574Asp | missense_variant, splice_region_variant | Exon 5 of 8 | XP_047292804.1 | ||
FAAP100 | NR_033338.2 | n.2393G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 6 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000221 AC: 53AN: 240006Hom.: 0 AF XY: 0.000206 AC XY: 27AN XY: 131100
GnomAD4 exome AF: 0.000138 AC: 200AN: 1452790Hom.: 0 Cov.: 31 AF XY: 0.000124 AC XY: 90AN XY: 722932
GnomAD4 genome AF: 0.000138 AC: 21AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2174G>A (p.G725D) alteration is located in exon 6 (coding exon 6) of the FAAP100 gene. This alteration results from a G to A substitution at nucleotide position 2174, causing the glycine (G) at amino acid position 725 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