chr1-154929156-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006556.4(PMVK):c.180G>T(p.Gln60His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006556.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMVK | NM_006556.4 | c.180G>T | p.Gln60His | missense_variant | 3/5 | ENST00000368467.4 | |
PMVK | NM_001323011.3 | c.138G>T | p.Gln46His | missense_variant | 3/5 | ||
PMVK | NM_001323012.3 | c.-46G>T | 5_prime_UTR_variant | 3/5 | |||
PMVK | NM_001348696.2 | c.54-99G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMVK | ENST00000368467.4 | c.180G>T | p.Gln60His | missense_variant | 3/5 | 1 | NM_006556.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727220
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.180G>T (p.Q60H) alteration is located in exon 3 (coding exon 3) of the PMVK gene. This alteration results from a G to T substitution at nucleotide position 180, causing the glutamine (Q) at amino acid position 60 to be replaced by a histidine (H). 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