rs145204580
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 5P and 12B. PM1PM2PP2BP4_StrongBP6_Very_Strong
The ENST00000358385.12(ATL1):c.306C>A(p.Asp102Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000855 in 1,613,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D102H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000358385.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL1 | NM_015915.5 | c.306C>A | p.Asp102Glu | missense_variant | 3/14 | ENST00000358385.12 | NP_056999.2 | |
ATL1 | NM_001127713.1 | c.306C>A | p.Asp102Glu | missense_variant | 4/14 | NP_001121185.1 | ||
ATL1 | NM_181598.4 | c.306C>A | p.Asp102Glu | missense_variant | 3/13 | NP_853629.2 | ||
ATL1 | XM_047431430.1 | c.306C>A | p.Asp102Glu | missense_variant | 4/15 | XP_047287386.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATL1 | ENST00000358385.12 | c.306C>A | p.Asp102Glu | missense_variant | 3/14 | 1 | NM_015915.5 | ENSP00000351155 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251250Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135796
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461574Hom.: 0 Cov.: 30 AF XY: 0.0000798 AC XY: 58AN XY: 727086
GnomAD4 genome AF: 0.000125 AC: 19AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74436
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 3A Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 17, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Neuropathy, hereditary sensory, type 1D Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 04, 2019 | This variant is associated with the following publications: (PMID: 28160950) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at