22-50744827-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001097.3(ACR):c.886A>G(p.Met296Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 1,600,480 control chromosomes in the GnomAD database, including 374,742 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 34480 hom., cov: 22)
Exomes 𝑓: 0.68 ( 340262 hom. )
Consequence
ACR
NM_001097.3 missense
NM_001097.3 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: -0.457
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.2673811E-6).
BP6
?
Variant 22-50744827-A-G is Benign according to our data. Variant chr22-50744827-A-G is described in ClinVar as [Benign]. Clinvar id is 402336.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACR | NM_001097.3 | c.886A>G | p.Met296Val | missense_variant | 5/5 | ENST00000216139.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACR | ENST00000216139.10 | c.886A>G | p.Met296Val | missense_variant | 5/5 | 1 | NM_001097.3 | P1 | |
ACR | ENST00000527761.1 | n.345A>G | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.680 AC: 100960AN: 148446Hom.: 34452 Cov.: 22
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GnomAD3 exomes AF: 0.712 AC: 136773AN: 192086Hom.: 48908 AF XY: 0.715 AC XY: 73632AN XY: 102976
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GnomAD4 exome AF: 0.683 AC: 991752AN: 1451922Hom.: 340262 Cov.: 47 AF XY: 0.687 AC XY: 495550AN XY: 721412
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GnomAD4 genome ? AF: 0.680 AC: 101030AN: 148558Hom.: 34480 Cov.: 22 AF XY: 0.683 AC XY: 49361AN XY: 72304
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 73% of total chromosomes in ExAC - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at