12-8648155-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BP6BS2
The NM_003480.4(MFAP5):c.458G>A(p.Arg153His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R153S) has been classified as Uncertain significance.
Frequency
Consequence
NM_003480.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251352Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135860
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461654Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727140
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74286
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The p.R153H variant (also known as c.458G>A), located in coding exon 9 of the MFAP5 gene, results from a G to A substitution at nucleotide position 458. The arginine at codon 153 is replaced by histidine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
not provided Benign:1
MFAP5: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at