1-156475126-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005920.4(MEF2D):c.988C>T(p.Pro330Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000193 in 1,614,084 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 Uncertain significance (★).
Frequency
Consequence
NM_005920.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEF2D | ENST00000348159.9 | c.988C>T | p.Pro330Ser | missense_variant | Exon 9 of 12 | 1 | NM_005920.4 | ENSP00000271555.5 | ||
MEF2D | ENST00000360595.7 | c.967C>T | p.Pro323Ser | missense_variant | Exon 8 of 11 | 1 | ENSP00000353803.3 | |||
MEF2D | ENST00000464356.6 | c.964C>T | p.Pro322Ser | missense_variant | Exon 7 of 10 | 5 | ENSP00000476788.1 | |||
MEF2D | ENST00000475587.2 | n.*224+1886C>T | intron_variant | Intron 6 of 8 | 5 | ENSP00000477413.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251414Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135876
GnomAD4 exome AF: 0.000200 AC: 292AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.000197 AC XY: 143AN XY: 727220
GnomAD4 genome AF: 0.000125 AC: 19AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.988C>T (p.P330S) alteration is located in exon 9 (coding exon 8) of the MEF2D gene. This alteration results from a C to T substitution at nucleotide position 988, causing the proline (P) at amino acid position 330 to be replaced by a serine (S). 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