1-16975337-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002403.4(MFAP2):c.380G>A(p.Arg127His) variant causes a missense change. The variant allele was found at a frequency of 0.000439 in 1,613,776 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002403.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MFAP2 | NM_002403.4 | c.380G>A | p.Arg127His | missense_variant | Exon 8 of 9 | ENST00000375535.4 | NP_002394.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MFAP2 | ENST00000375535.4 | c.380G>A | p.Arg127His | missense_variant | Exon 8 of 9 | 1 | NM_002403.4 | ENSP00000364685.3 | ||
MFAP2 | ENST00000375534.7 | c.377G>A | p.Arg126His | missense_variant | Exon 7 of 8 | 2 | ENSP00000364684.3 | |||
MFAP2 | ENST00000490075.5 | n.1781G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152092Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250586Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135464
GnomAD4 exome AF: 0.000471 AC: 689AN: 1461566Hom.: 2 Cov.: 35 AF XY: 0.000435 AC XY: 316AN XY: 727102
GnomAD4 genome AF: 0.000131 AC: 20AN: 152210Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.380G>A (p.R127H) alteration is located in exon 8 (coding exon 7) of the MFAP2 gene. This alteration results from a G to A substitution at nucleotide position 380, causing the arginine (R) at amino acid position 127 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