rs12590500
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001113498.3(MDGA2):c.2029G>T(p.Val677Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 1,613,874 control chromosomes in the GnomAD database, including 6,663 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001113498.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MDGA2 | NM_001113498.3 | c.2029G>T | p.Val677Phe | missense_variant | 9/17 | ENST00000399232.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDGA2 | ENST00000399232.8 | c.2029G>T | p.Val677Phe | missense_variant | 9/17 | 1 | NM_001113498.3 | P1 | |
MDGA2 | ENST00000357362.7 | c.1135G>T | p.Val379Phe | missense_variant | 9/17 | 5 | |||
MDGA2 | ENST00000557238.5 | c.*407G>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17825AN: 151956Hom.: 1979 Cov.: 32
GnomAD3 exomes AF: 0.0960 AC: 23935AN: 249318Hom.: 2567 AF XY: 0.0843 AC XY: 11400AN XY: 135260
GnomAD4 exome AF: 0.0479 AC: 70048AN: 1461800Hom.: 4663 Cov.: 31 AF XY: 0.0474 AC XY: 34457AN XY: 727206
GnomAD4 genome ? AF: 0.118 AC: 17899AN: 152074Hom.: 2000 Cov.: 32 AF XY: 0.121 AC XY: 8990AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at