NM_001166114.2:c.3954C>T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001166114.2(PNPLA6):c.3954C>T(p.Ala1318Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000891 in 1,610,718 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001166114.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNPLA6 | NM_001166114.2 | c.3954C>T | p.Ala1318Ala | synonymous_variant | Exon 31 of 32 | ENST00000600737.6 | NP_001159586.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNPLA6 | ENST00000600737.6 | c.3954C>T | p.Ala1318Ala | synonymous_variant | Exon 31 of 32 | 1 | NM_001166114.2 | ENSP00000473211.1 |
Frequencies
GnomAD3 genomes AF: 0.00382 AC: 581AN: 152092Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00117 AC: 282AN: 242008Hom.: 1 AF XY: 0.000916 AC XY: 120AN XY: 131020
GnomAD4 exome AF: 0.000585 AC: 853AN: 1458508Hom.: 3 Cov.: 33 AF XY: 0.000535 AC XY: 388AN XY: 725238
GnomAD4 genome AF: 0.00382 AC: 582AN: 152210Hom.: 5 Cov.: 33 AF XY: 0.00378 AC XY: 281AN XY: 74412
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 39 Uncertain:1Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not specified Benign:1
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Hereditary spastic paraplegia Benign:1
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PNPLA6-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at