rs148544851
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_006556.4(PMVK):c.223G>C(p.Asp75His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PMVK | NM_006556.4 | c.223G>C | p.Asp75His | missense_variant | Exon 3 of 5 | ENST00000368467.4 | NP_006547.1 | |
PMVK | NM_001323011.3 | c.181G>C | p.Asp61His | missense_variant | Exon 3 of 5 | NP_001309940.1 | ||
PMVK | NM_001323012.3 | c.-3G>C | 5_prime_UTR_variant | Exon 3 of 5 | NP_001309941.1 | |||
PMVK | NM_001348696.2 | c.54-56G>C | intron_variant | Intron 2 of 4 | NP_001335625.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251490Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135920
GnomAD4 exome AF: 0.000187 AC: 274AN: 1461848Hom.: 0 Cov.: 30 AF XY: 0.000191 AC XY: 139AN XY: 727238
GnomAD4 genome AF: 0.000151 AC: 23AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.223G>C (p.D75H) alteration is located in exon 3 (coding exon 3) of the PMVK gene. This alteration results from a G to C substitution at nucleotide position 223, causing the aspartic acid (D) at amino acid position 75 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