22-44093970-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013327.5(PARVB):c.155C>G(p.Pro52Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00364 in 1,613,610 control chromosomes in the GnomAD database, including 198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.019 ( 105 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 93 hom. )
Consequence
PARVB
NM_013327.5 missense
NM_013327.5 missense
Scores
3
7
6
Clinical Significance
Conservation
PhyloP100: 5.66
Genes affected
PARVB (HGNC:14653): (parvin beta) This gene encodes a member of the parvin family of actin-binding proteins, which play a role in cytoskeleton organization and cell adhesion. These proteins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. This family member binds to alphaPIX and alpha-actinin, and it can inhibit the activity of integrin-linked kinase. This protein also functions in tumor suppression. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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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=0.0026082397).
BP6
?
Variant 22-44093970-C-G is Benign according to our data. Variant chr22-44093970-C-G is described in ClinVar as [Benign]. Clinvar id is 777733.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARVB | NM_013327.5 | c.155C>G | p.Pro52Arg | missense_variant | 2/13 | ENST00000338758.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARVB | ENST00000338758.12 | c.155C>G | p.Pro52Arg | missense_variant | 2/13 | 1 | NM_013327.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2867AN: 152206Hom.: 104 Cov.: 33
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GnomAD3 exomes AF: 0.00505 AC: 1268AN: 251300Hom.: 36 AF XY: 0.00356 AC XY: 483AN XY: 135814
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GnomAD4 exome AF: 0.00205 AC: 2999AN: 1461286Hom.: 93 Cov.: 29 AF XY: 0.00177 AC XY: 1289AN XY: 727006
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GnomAD4 genome ? AF: 0.0189 AC: 2879AN: 152324Hom.: 105 Cov.: 33 AF XY: 0.0180 AC XY: 1338AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Benign
D;D;D;T
Sift4G
Uncertain
T;D;D;.
Polyphen
D;D;.;.
Vest4
MVP
MPC
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