rs34745784
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022786.3(ARV1):c.94T>C(p.Tyr32His) variant causes a missense change. The variant allele was found at a frequency of 0.00171 in 1,613,546 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0090 ( 20 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 24 hom. )
Consequence
ARV1
NM_022786.3 missense
NM_022786.3 missense
Scores
4
7
7
Clinical Significance
Conservation
PhyloP100: 6.65
Genes affected
ARV1 (HGNC:29561): (ARV1 homolog, fatty acid homeostasis modulator) this gene encodes a transmembrane protein that contains a conserved zinc ribbon motif at the N- terminus. A similar protein in mouse is thought to function in fatty acid homeostasis. Mutations in this gene are associated with early infantile epileptic encephalopathy 38. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009450704).
BP6
?
Variant 1-230979199-T-C is Benign according to our data. Variant chr1-230979199-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 445383.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00897 (1366/152228) while in subpopulation AFR AF= 0.0311 (1293/41538). AF 95% confidence interval is 0.0297. There are 20 homozygotes in gnomad4. There are 646 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARV1 | NM_022786.3 | c.94T>C | p.Tyr32His | missense_variant | 1/6 | ENST00000310256.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARV1 | ENST00000310256.7 | c.94T>C | p.Tyr32His | missense_variant | 1/6 | 1 | NM_022786.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00896 AC: 1363AN: 152110Hom.: 20 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00237 AC: 594AN: 250618Hom.: 11 AF XY: 0.00176 AC XY: 239AN XY: 135510
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GnomAD4 exome AF: 0.000951 AC: 1389AN: 1461318Hom.: 24 Cov.: 31 AF XY: 0.000825 AC XY: 600AN XY: 726982
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GnomAD4 genome ? AF: 0.00897 AC: 1366AN: 152228Hom.: 20 Cov.: 32 AF XY: 0.00868 AC XY: 646AN XY: 74424
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ESP6500AA
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ExAC
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334
Asia WGS
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3478
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 22, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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