NM_001388490.1:c.310C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001388490.1(MAP7D1):c.310C>T(p.Arg104Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00277 in 1,610,352 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0027 ( 6 hom., cov: 31)
Exomes 𝑓: 0.0028 ( 81 hom. )
Consequence
MAP7D1
NM_001388490.1 missense
NM_001388490.1 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 0.699
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0029316545).
BP6
Variant 1-36171234-C-T is Benign according to our data. Variant chr1-36171234-C-T is described in ClinVar as [Benign]. Clinvar id is 713175.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00267 (407/152254) while in subpopulation EAS AF= 0.0443 (229/5166). AF 95% confidence interval is 0.0396. There are 6 homozygotes in gnomad4. There are 214 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP7D1 | NM_001388490.1 | c.310C>T | p.Arg104Trp | missense_variant | Exon 2 of 17 | ENST00000474796.2 | NP_001375419.1 | |
MAP7D1 | NM_018067.5 | c.310C>T | p.Arg104Trp | missense_variant | Exon 2 of 17 | NP_060537.3 | ||
MAP7D1 | NM_001286366.2 | c.310C>T | p.Arg104Trp | missense_variant | Exon 2 of 18 | NP_001273295.1 | ||
MAP7D1 | NM_001286365.2 | c.310C>T | p.Arg104Trp | missense_variant | Exon 2 of 16 | NP_001273294.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00268 AC: 408AN: 152136Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.00646 AC: 1589AN: 245926Hom.: 34 AF XY: 0.00676 AC XY: 901AN XY: 133328
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GnomAD4 exome AF: 0.00278 AC: 4051AN: 1458098Hom.: 81 Cov.: 33 AF XY: 0.00323 AC XY: 2341AN XY: 725216
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GnomAD4 genome AF: 0.00267 AC: 407AN: 152254Hom.: 6 Cov.: 31 AF XY: 0.00287 AC XY: 214AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;L;L;.
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.99, 1.0
.;D;D;D;.
Vest4
0.28, 0.31, 0.28
MVP
MPC
0.57
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at