chr17-7344554-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014716.4(ACAP1):c.760G>A(p.Glu254Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000903 in 1,551,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAP1 | NM_014716.4 | c.760G>A | p.Glu254Lys | missense_variant | 10/22 | ENST00000158762.8 | |
ACAP1 | XM_047437150.1 | c.538G>A | p.Glu180Lys | missense_variant | 10/22 | ||
ACAP1 | XM_047437151.1 | c.538G>A | p.Glu180Lys | missense_variant | 9/21 | ||
ACAP1 | XM_047437152.1 | c.760G>A | p.Glu254Lys | missense_variant | 10/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAP1 | ENST00000158762.8 | c.760G>A | p.Glu254Lys | missense_variant | 10/22 | 1 | NM_014716.4 | P1 | |
ACAP1 | ENST00000571220.1 | n.860G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000640 AC: 1AN: 156360Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 82276
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1398934Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 689972
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.760G>A (p.E254K) alteration is located in exon 10 (coding exon 10) of the ACAP1 gene. This alteration results from a G to A substitution at nucleotide position 760, causing the glutamic acid (E) at amino acid position 254 to be replaced by a lysine (K). 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