X-20012356-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001168465.2(MAP7D2):c.2065G>A(p.Asp689Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000461 in 1,083,892 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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.2065G>A | p.Asp689Asn | missense_variant | Exon 15 of 17 | 1 | NM_001168465.2 | ENSP00000368964.5 | ||
MAP7D2 | ENST00000379651.7 | c.1942G>A | p.Asp648Asn | missense_variant | Exon 14 of 16 | 1 | ENSP00000368972.3 | |||
MAP7D2 | ENST00000443379.7 | c.1807G>A | p.Asp603Asn | missense_variant | Exon 13 of 15 | 2 | ENSP00000388239.3 | |||
MAP7D2 | ENST00000452324.3 | c.1786G>A | p.Asp596Asn | missense_variant | Exon 14 of 16 | 2 | ENSP00000413301.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000461 AC: 5AN: 1083892Hom.: 0 Cov.: 28 AF XY: 0.00000855 AC XY: 3AN XY: 350954
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2065G>A (p.D689N) alteration is located in exon 15 (coding exon 15) of the MAP7D2 gene. This alteration results from a G to A substitution at nucleotide position 2065, causing the aspartic acid (D) at amino acid position 689 to be replaced by an asparagine (N). 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
Publications
No publications associated with this variant yet.