22-50744956-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001097.3(ACR):c.1015C>A(p.Pro339Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 13)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACR
NM_001097.3 missense
NM_001097.3 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 0.00300
Genes affected
ACR (HGNC:126): (acrosin) Acrosin is the major proteinase present in the acrosome of mature spermatozoa. It is a typical serine proteinase with trypsin-like specificity. It is stored in the acrosome in its precursor form, proacrosin. The active enzyme functions in the lysis of the zona pellucida, thus facilitating penetration of the sperm through the innermost glycoprotein layers of the ovum. The mRNA for proacrosin is synthesized only in the postmeiotic stages of spermatogenesis. In humans proacrosin first appears in the haploid spermatids. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.30870265).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACR | NM_001097.3 | c.1015C>A | p.Pro339Thr | missense_variant | 5/5 | ENST00000216139.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACR | ENST00000216139.10 | c.1015C>A | p.Pro339Thr | missense_variant | 5/5 | 1 | NM_001097.3 | P1 | |
ACR | ENST00000527761.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 13
GnomAD3 genomes
?
Cov.:
13
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000681 AC: 9AN: 1321258Hom.: 0 Cov.: 28 AF XY: 0.00000463 AC XY: 3AN XY: 648454
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
9
AN:
1321258
Hom.:
Cov.:
28
AF XY:
AC XY:
3
AN XY:
648454
Gnomad4 AFR exome
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Gnomad4 FIN exome
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GnomAD4 genome ? Cov.: 13
GnomAD4 genome
?
Cov.:
13
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.1015C>A (p.P339T) alteration is located in exon 5 (coding exon 5) of the ACR gene. This alteration results from a C to A substitution at nucleotide position 1015, causing the proline (P) at amino acid position 339 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
M
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of phosphorylation at P339 (P = 0.0023);
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at