X-136220923-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024597.4(MAP7D3):c.2328G>A(p.Met776Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,207,209 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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 Likely benign (★).
Frequency
Consequence
NM_024597.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP7D3 | NM_024597.4 | c.2328G>A | p.Met776Ile | missense_variant | Exon 16 of 19 | ENST00000316077.14 | NP_078873.2 | |
MAP7D3 | NM_001173516.1 | c.2274G>A | p.Met758Ile | missense_variant | Exon 16 of 19 | NP_001166987.1 | ||
MAP7D3 | NM_001173517.2 | c.2223G>A | p.Met741Ile | missense_variant | Exon 15 of 18 | NP_001166988.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111946Hom.: 0 Cov.: 24 AF XY: 0.0000293 AC XY: 1AN XY: 34132
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181677Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67539
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1095263Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 1AN XY: 360687
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111946Hom.: 0 Cov.: 24 AF XY: 0.0000293 AC XY: 1AN XY: 34132
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at