rs149376662
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_031433.4(MFRP):c.191G>A(p.Arg64His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000978 in 1,603,600 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R64C) has been classified as Uncertain significance.
Frequency
Consequence
NM_031433.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFRP | NM_031433.4 | c.191G>A | p.Arg64His | missense_variant | 3/15 | ENST00000619721.6 | |
C1QTNF5 | NM_015645.5 | c.-2446G>A | 5_prime_UTR_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFRP | ENST00000619721.6 | c.191G>A | p.Arg64His | missense_variant | 3/15 | 1 | NM_031433.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00105 AC: 160AN: 152106Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00151 AC: 341AN: 225536Hom.: 3 AF XY: 0.00147 AC XY: 180AN XY: 122226
GnomAD4 exome AF: 0.000970 AC: 1408AN: 1451376Hom.: 13 Cov.: 36 AF XY: 0.000984 AC XY: 709AN XY: 720874
GnomAD4 genome ? AF: 0.00105 AC: 160AN: 152224Hom.: 2 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74442
ClinVar
Submissions by phenotype
Isolated microphthalmia 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Retinal degeneration Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Isolated microphthalmia 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at