6-136361088-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003980.6(MAP7):āc.1618C>Gā(p.Arg540Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,604,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003980.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP7 | NM_003980.6 | c.1618C>G | p.Arg540Gly | missense_variant | 12/18 | ENST00000354570.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP7 | ENST00000354570.8 | c.1618C>G | p.Arg540Gly | missense_variant | 12/18 | 1 | NM_003980.6 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000421 AC: 10AN: 237698Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130496
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1451822Hom.: 0 Cov.: 35 AF XY: 0.00000830 AC XY: 6AN XY: 722572
GnomAD4 genome AF: 0.000158 AC: 24AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1708C>G (p.R570G) alteration is located in exon 12 (coding exon 12) of the MAP7 gene. This alteration results from a C to G substitution at nucleotide position 1708, causing the arginine (R) at amino acid position 570 to be replaced by a glycine (G). 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