ENST00000562145.1:n.1142G>T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000562145.1(FA2H):n.1142G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 393,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000562145.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
- hereditary spastic paraplegia 35Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FA2H | ENST00000562145.1 | n.1142G>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
FA2H | ENST00000219368.8 | c.*302G>T | 3_prime_UTR_variant | Exon 7 of 7 | 1 | NM_024306.5 | ENSP00000219368.3 | |||
FA2H | ENST00000567683.5 | n.*700G>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 | ENSP00000455126.1 | ||||
FA2H | ENST00000567683.5 | n.*700G>T | 3_prime_UTR_variant | Exon 5 of 5 | 2 | ENSP00000455126.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 33 show subpopulations
GnomAD4 exome AF: 0.00000414 AC: 1AN: 241680Hom.: 0 Cov.: 0 AF XY: 0.00000804 AC XY: 1AN XY: 124438 show subpopulations
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at