6-151458515-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001286562.2(ARMT1):c.-23C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001286562.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMT1 | NM_024573.3 | c.335C>T | p.Pro112Leu | missense_variant | Exon 3 of 5 | ENST00000367294.4 | NP_078849.1 | |
ARMT1 | NM_001286562.2 | c.-23C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 4 | NP_001273491.1 | |||
ARMT1 | NM_001286562.2 | c.-23C>T | 5_prime_UTR_variant | Exon 2 of 4 | NP_001273491.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251222Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135792
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459216Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726104
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.335C>T (p.P112L) alteration is located in exon 3 (coding exon 3) of the ARMT1 gene. This alteration results from a C to T substitution at nucleotide position 335, causing the proline (P) at amino acid position 112 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at