X-20011024-T-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001168465.2(MAP7D2):āc.2101A>Cā(p.Ile701Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000232 in 1,208,586 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00016 ( 0 hom., 3 hem., cov: 23)
Exomes š: 0.0000091 ( 0 hom. 3 hem. )
Consequence
MAP7D2
NM_001168465.2 missense
NM_001168465.2 missense
Scores
2
8
7
Clinical Significance
Conservation
PhyloP100: 6.91
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.24173322).
BS2
High Hemizygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP7D2 | NM_001168465.2 | c.2101A>C | p.Ile701Leu | missense_variant | 16/17 | ENST00000379643.10 | NP_001161937.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP7D2 | ENST00000379643.10 | c.2101A>C | p.Ile701Leu | missense_variant | 16/17 | 1 | NM_001168465.2 | ENSP00000368964 | A2 | |
MAP7D2 | ENST00000379651.7 | c.1978A>C | p.Ile660Leu | missense_variant | 15/16 | 1 | ENSP00000368972 | A2 | ||
MAP7D2 | ENST00000443379.7 | c.1843A>C | p.Ile615Leu | missense_variant | 14/15 | 2 | ENSP00000388239 | A2 | ||
MAP7D2 | ENST00000452324.3 | c.1822A>C | p.Ile608Leu | missense_variant | 15/16 | 2 | ENSP00000413301 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000161 AC: 18AN: 111700Hom.: 0 Cov.: 23 AF XY: 0.0000885 AC XY: 3AN XY: 33890
GnomAD3 genomes
AF:
AC:
18
AN:
111700
Hom.:
Cov.:
23
AF XY:
AC XY:
3
AN XY:
33890
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000383 AC: 7AN: 182991Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67537
GnomAD3 exomes
AF:
AC:
7
AN:
182991
Hom.:
AF XY:
AC XY:
0
AN XY:
67537
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000912 AC: 10AN: 1096886Hom.: 0 Cov.: 29 AF XY: 0.00000828 AC XY: 3AN XY: 362266
GnomAD4 exome
AF:
AC:
10
AN:
1096886
Hom.:
Cov.:
29
AF XY:
AC XY:
3
AN XY:
362266
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000161 AC: 18AN: 111700Hom.: 0 Cov.: 23 AF XY: 0.0000885 AC XY: 3AN XY: 33890
GnomAD4 genome
AF:
AC:
18
AN:
111700
Hom.:
Cov.:
23
AF XY:
AC XY:
3
AN XY:
33890
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
4
ESP6500EA
AF:
AC:
0
ExAC
AF:
AC:
8
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2022 | The c.2101A>C (p.I701L) alteration is located in exon 16 (coding exon 16) of the MAP7D2 gene. This alteration results from a A to C substitution at nucleotide position 2101, causing the isoleucine (I) at amino acid position 701 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
D;D;.;.
Vest4
MVP
MPC
0.12
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at