NM_001388490.1:c.310C>T

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

Scores

5
13

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.699
Variant links:
Genes affected
MAP7D1 (HGNC:25514): (MAP7 domain containing 1) Predicted to be involved in microtubule cytoskeleton organization. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

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
MAP7D1NM_001388490.1 linkc.310C>T p.Arg104Trp missense_variant Exon 2 of 17 ENST00000474796.2 NP_001375419.1
MAP7D1NM_018067.5 linkc.310C>T p.Arg104Trp missense_variant Exon 2 of 17 NP_060537.3 Q3KQU3-1
MAP7D1NM_001286366.2 linkc.310C>T p.Arg104Trp missense_variant Exon 2 of 18 NP_001273295.1 Q3KQU3-4B3KU03
MAP7D1NM_001286365.2 linkc.310C>T p.Arg104Trp missense_variant Exon 2 of 16 NP_001273294.1 Q3KQU3-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAP7D1ENST00000474796.2 linkc.310C>T p.Arg104Trp missense_variant Exon 2 of 17 2 NM_001388490.1 ENSP00000507044.1 D3DPS3

Frequencies

GnomAD3 genomes
AF:
0.00268
AC:
408
AN:
152136
Hom.:
5
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000941
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00111
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0442
Gnomad SAS
AF:
0.0209
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000279
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00646
AC:
1589
AN:
245926
Hom.:
34
AF XY:
0.00676
AC XY:
901
AN XY:
133328
show subpopulations
Gnomad AFR exome
AF:
0.000879
Gnomad AMR exome
AF:
0.000414
Gnomad ASJ exome
AF:
0.000621
Gnomad EAS exome
AF:
0.0436
Gnomad SAS exome
AF:
0.0227
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000362
Gnomad OTH exome
AF:
0.00552
GnomAD4 exome
AF:
0.00278
AC:
4051
AN:
1458098
Hom.:
81
Cov.:
33
AF XY:
0.00323
AC XY:
2341
AN XY:
725216
show subpopulations
Gnomad4 AFR exome
AF:
0.000420
Gnomad4 AMR exome
AF:
0.000431
Gnomad4 ASJ exome
AF:
0.000426
Gnomad4 EAS exome
AF:
0.0386
Gnomad4 SAS exome
AF:
0.0219
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000208
Gnomad4 OTH exome
AF:
0.00578
GnomAD4 genome
AF:
0.00267
AC:
407
AN:
152254
Hom.:
6
Cov.:
31
AF XY:
0.00287
AC XY:
214
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.000939
Gnomad4 AMR
AF:
0.00111
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0443
Gnomad4 SAS
AF:
0.0207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000279
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00151
Hom.:
3
Bravo
AF:
0.00228
TwinsUK
AF:
0.000539
AC:
2
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00114
AC:
5
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00629
AC:
764
Asia WGS
AF:
0.0320
AC:
113
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000119

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.49
T
BayesDel_noAF
Benign
-0.45
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.022
.;.;.;T;.
Eigen
Benign
-0.12
Eigen_PC
Benign
-0.21
FATHMM_MKL
Benign
0.16
N
LIST_S2
Uncertain
0.95
D;D;D;D;D
MetaRNN
Benign
0.0029
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.5
.;L;L;L;.
PrimateAI
Benign
0.45
T
PROVEAN
Uncertain
-3.0
D;D;D;D;D
REVEL
Benign
0.099
Sift
Uncertain
0.0020
D;D;D;D;D
Sift4G
Uncertain
0.014
D;D;D;D;D
Polyphen
0.99, 1.0
.;D;D;D;.
Vest4
0.28, 0.31, 0.28
MVP
0.082
MPC
0.57
ClinPred
0.036
T
GERP RS
2.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.17
gMVP
0.19

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2296266; hg19: chr1-36636835; COSMIC: COSV60216630; COSMIC: COSV60216630; API