14-50587817-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015915.5(ATL1):c.35-14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,614,164 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015915.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATL1 | NM_015915.5 | c.35-14G>A | intron_variant | Intron 1 of 13 | ENST00000358385.12 | NP_056999.2 | ||
ATL1 | NM_001127713.1 | c.35-14G>A | intron_variant | Intron 2 of 13 | NP_001121185.1 | |||
ATL1 | NM_181598.4 | c.35-14G>A | intron_variant | Intron 1 of 12 | NP_853629.2 | |||
ATL1 | XM_047431430.1 | c.35-14G>A | intron_variant | Intron 2 of 14 | XP_047287386.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00834 AC: 1269AN: 152214Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00219 AC: 550AN: 251250Hom.: 6 AF XY: 0.00152 AC XY: 207AN XY: 135828
GnomAD4 exome AF: 0.000788 AC: 1152AN: 1461832Hom.: 11 Cov.: 31 AF XY: 0.000624 AC XY: 454AN XY: 727218
GnomAD4 genome AF: 0.00834 AC: 1271AN: 152332Hom.: 15 Cov.: 32 AF XY: 0.00828 AC XY: 617AN XY: 74476
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 3A Benign:2
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not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Neuropathy, hereditary sensory, type 1D Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at