chr11-63629346-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015459.5(ATL3):āc.1599A>Gā(p.Arg533=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,614,128 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0026 ( 12 hom., cov: 31)
Exomes š: 0.0046 ( 279 hom. )
Consequence
ATL3
NM_015459.5 synonymous
NM_015459.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.464
Genes affected
ATL3 (HGNC:24526): (atlastin GTPase 3) This gene encodes a member of a family of dynamin-like, integral membrane GTPases. The encoded protein is required for the proper formation of the network of interconnected tubules of the endoplasmic reticulum. Mutations in this gene may be associated with hereditary sensory neuropathy type IF. Alternatively spliced transcript variants that encode distinct isoforms have been described. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 11-63629346-T-C is Benign according to our data. Variant chr11-63629346-T-C is described in ClinVar as [Benign]. Clinvar id is 474837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-63629346-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.464 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL3 | NM_015459.5 | c.1599A>G | p.Arg533= | synonymous_variant | 13/13 | ENST00000398868.8 | NP_056274.3 | |
ATL3 | NM_001290048.2 | c.1545A>G | p.Arg515= | synonymous_variant | 13/13 | NP_001276977.1 | ||
ATL3 | XM_047426725.1 | c.1755A>G | p.Arg585= | synonymous_variant | 14/14 | XP_047282681.1 | ||
ATL3 | XM_006718493.2 | c.1542A>G | p.Arg514= | synonymous_variant | 12/12 | XP_006718556.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATL3 | ENST00000398868.8 | c.1599A>G | p.Arg533= | synonymous_variant | 13/13 | 1 | NM_015459.5 | ENSP00000381844 | ||
ATL3 | ENST00000538786.1 | c.1545A>G | p.Arg515= | synonymous_variant | 13/13 | 2 | ENSP00000437593 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00264 AC: 402AN: 152180Hom.: 12 Cov.: 31
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GnomAD3 exomes AF: 0.00927 AC: 2313AN: 249570Hom.: 94 AF XY: 0.0123 AC XY: 1662AN XY: 135406
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GnomAD4 exome AF: 0.00464 AC: 6781AN: 1461830Hom.: 279 Cov.: 30 AF XY: 0.00669 AC XY: 4863AN XY: 727220
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GnomAD4 genome AF: 0.00264 AC: 402AN: 152298Hom.: 12 Cov.: 31 AF XY: 0.00384 AC XY: 286AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Neuropathy, hereditary sensory, type 1F Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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