17-7342009-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014716.4(ACAP1):c.173C>A(p.Ala58Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,090 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_014716.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAP1 | NM_014716.4 | c.173C>A | p.Ala58Asp | missense_variant | 3/22 | ENST00000158762.8 | |
ACAP1 | XM_047437152.1 | c.173C>A | p.Ala58Asp | missense_variant | 3/18 | ||
ACAP1 | XM_047437150.1 | c.-50C>A | 5_prime_UTR_variant | 3/22 | |||
ACAP1 | XM_047437151.1 | c.-50C>A | 5_prime_UTR_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAP1 | ENST00000158762.8 | c.173C>A | p.Ala58Asp | missense_variant | 3/22 | 1 | NM_014716.4 | P1 | |
ACAP1 | ENST00000570457.6 | c.-50C>A | 5_prime_UTR_variant | 3/8 | 5 | ||||
ACAP1 | ENST00000575425.1 | c.-50C>A | 5_prime_UTR_variant | 2/5 | 3 | ||||
ACAP1 | ENST00000576628.1 | n.311C>A | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251438Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135888
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727246
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.173C>A (p.A58D) alteration is located in exon 3 (coding exon 3) of the ACAP1 gene. This alteration results from a C to A substitution at nucleotide position 173, causing the alanine (A) at amino acid position 58 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