14-67620954-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001172.4(ARG2):c.172C>T(p.Leu58Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L58V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001172.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARG2 | NM_001172.4 | c.172C>T | p.Leu58Phe | missense_variant | Exon 2 of 8 | ENST00000261783.4 | NP_001163.1 | |
GPHN | XM_047430879.1 | c.1313-114241C>T | intron_variant | Intron 14 of 14 | XP_047286835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARG2 | ENST00000261783.4 | c.172C>T | p.Leu58Phe | missense_variant | Exon 2 of 8 | 1 | NM_001172.4 | ENSP00000261783.3 | ||
ARG2 | ENST00000556491.1 | n.170C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | |||||
ARG2 | ENST00000557120.5 | n.214C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461808Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727200
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at