chr2-86216945-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_001371279.1(REEP1):c.*94T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 1,019,268 control chromosomes in the GnomAD database, including 506 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_001371279.1 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
REEP1 | NM_001371279.1 | c.*94T>C | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000538924.7 | NP_001358208.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REEP1 | ENST00000538924 | c.*94T>C | 3_prime_UTR_variant | Exon 9 of 9 | 5 | NM_001371279.1 | ENSP00000438346.3 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 3318AN: 152154Hom.: 69 Cov.: 32
GnomAD4 exome AF: 0.0278 AC: 24094AN: 866996Hom.: 437 Cov.: 12 AF XY: 0.0270 AC XY: 12115AN XY: 448970
GnomAD4 genome AF: 0.0218 AC: 3318AN: 152272Hom.: 69 Cov.: 32 AF XY: 0.0212 AC XY: 1577AN XY: 74470
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1
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Hereditary spastic paraplegia 31 Benign:1
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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at