chr14-50632303-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_015915.5(ATL1):c.1641G>A(p.Ser547Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015915.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL1 | NM_015915.5 | c.1641G>A | p.Ser547Ser | synonymous_variant | Exon 14 of 14 | ENST00000358385.12 | NP_056999.2 | |
ATL1 | NM_001127713.1 | c.1626G>A | p.Ser542Ser | synonymous_variant | Exon 14 of 14 | NP_001121185.1 | ||
ATL1 | NM_181598.4 | c.1626G>A | p.Ser542Ser | synonymous_variant | Exon 13 of 13 | NP_853629.2 | ||
ATL1 | XM_047431430.1 | c.1641G>A | p.Ser547Ser | synonymous_variant | Exon 15 of 15 | XP_047287386.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250838Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135540
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460906Hom.: 0 Cov.: 30 AF XY: 0.0000399 AC XY: 29AN XY: 726806
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 3A Benign:1
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Inborn genetic diseases Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at