X-136225967-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024597.4(MAP7D3):c.2081A>G(p.Lys694Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,204,925 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.2081A>G | p.Lys694Arg | missense_variant | Exon 13 of 19 | ENST00000316077.14 | NP_078873.2 | |
MAP7D3 | NM_001173516.1 | c.2027A>G | p.Lys676Arg | missense_variant | Exon 13 of 19 | NP_001166987.1 | ||
MAP7D3 | NM_001173517.2 | c.1976A>G | p.Lys659Arg | missense_variant | Exon 12 of 18 | NP_001166988.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111959Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34105
GnomAD3 exomes AF: 0.0000286 AC: 5AN: 175014Hom.: 0 AF XY: 0.0000326 AC XY: 2AN XY: 61278
GnomAD4 exome AF: 0.000166 AC: 181AN: 1092966Hom.: 0 Cov.: 27 AF XY: 0.000114 AC XY: 41AN XY: 358598
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111959Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34105
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2081A>G (p.K694R) alteration is located in exon 13 (coding exon 13) of the MAP7D3 gene. This alteration results from a A to G substitution at nucleotide position 2081, causing the lysine (K) at amino acid position 694 to be replaced by an arginine (R). 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