X-20015281-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001168465.2(MAP7D2):c.1691G>A(p.Arg564His) variant causes a missense change. The variant allele was found at a frequency of 0.0000215 in 1,209,468 control chromosomes in the GnomAD database, including 1 homozygotes. There are 6 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R564S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001168465.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP7D2 | ENST00000379643.10 | c.1691G>A | p.Arg564His | missense_variant | Exon 12 of 17 | 1 | NM_001168465.2 | ENSP00000368964.5 | ||
MAP7D2 | ENST00000379651.7 | c.1568G>A | p.Arg523His | missense_variant | Exon 11 of 16 | 1 | ENSP00000368972.3 | |||
MAP7D2 | ENST00000443379.7 | c.1433G>A | p.Arg478His | missense_variant | Exon 10 of 15 | 2 | ENSP00000388239.3 | |||
MAP7D2 | ENST00000452324.3 | c.1412G>A | p.Arg471His | missense_variant | Exon 11 of 16 | 2 | ENSP00000413301.3 |
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111844Hom.: 0 Cov.: 24 AF XY: 0.0000588 AC XY: 2AN XY: 34002
GnomAD3 exomes AF: 0.0000656 AC: 12AN: 183057Hom.: 1 AF XY: 0.0000296 AC XY: 2AN XY: 67545
GnomAD4 exome AF: 0.0000200 AC: 22AN: 1097624Hom.: 1 Cov.: 29 AF XY: 0.0000110 AC XY: 4AN XY: 363012
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111844Hom.: 0 Cov.: 24 AF XY: 0.0000588 AC XY: 2AN XY: 34002
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1691G>A (p.R564H) alteration is located in exon 12 (coding exon 12) of the MAP7D2 gene. This alteration results from a G to A substitution at nucleotide position 1691, causing the arginine (R) at amino acid position 564 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