chr5-132294369-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000471826.1(P4HA2):n.138+809G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000722 in 554,094 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
ENST00000471826.1 intron, non_coding_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A4 | NM_003059.3 | upstream_gene_variant | ENST00000200652.4 | ||||
SLC22A4 | XM_006714675.5 | upstream_gene_variant | |||||
SLC22A4 | XM_011543589.3 | upstream_gene_variant | |||||
SLC22A4 | XM_047417594.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P4HA2 | ENST00000471826.1 | n.138+809G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
P4HA2 | ENST00000431054.5 | c.78+809G>A | intron_variant | 4 | |||||
SLC22A4 | ENST00000200652.4 | upstream_gene_variant | 1 | NM_003059.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151868Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000497 AC: 2AN: 402226Hom.: 0 AF XY: 0.00000948 AC XY: 2AN XY: 211052
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151868Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74168
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at