Variant 1-36171228-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001388490.1(MAP7D1):c.304G>C(p.Gly102Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,998 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 (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

MAP7D1
NM_001388490.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0800

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]

MAP7D1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.1529584).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MAP7D1	NM_001388490.1 linkuse as main transcript	c.304G>C	p.Gly102Arg	missense_variant	2/17	ENST00000474796.2	NP_001375419.1
MAP7D1	NM_018067.5 linkuse as main transcript	c.304G>C	p.Gly102Arg	missense_variant	2/17		NP_060537.3
MAP7D1	NM_001286366.2 linkuse as main transcript	c.304G>C	p.Gly102Arg	missense_variant	2/18		NP_001273295.1
MAP7D1	NM_001286365.2 linkuse as main transcript	c.304G>C	p.Gly102Arg	missense_variant	2/16		NP_001273294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP7D1	ENST00000474796.2 linkuse as main transcript	c.304G>C	p.Gly102Arg	missense_variant	2/17	2	NM_001388490.1	ENSP00000507044	A2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000405

AC:

AN:

246926

Hom.:

AF XY:

0.00000747

AC XY:

AN XY:

133804

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000548

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000206

AC:

AN:

1458998

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

725684

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

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

Mar 16, 2024

The c.304G>C (p.G102R) alteration is located in exon 2 (coding exon 2) of the MAP7D1 gene. This alteration results from a G to C substitution at nucleotide position 304, causing the glycine (G) at amino acid position 102 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.0081

.;.;.;T;.

Eigen

Benign

-0.063

Eigen_PC

Benign

-0.15

FATHMM_MKL

Benign

0.14

LIST_S2

Uncertain

0.93

D;D;D;D;D

M_CAP

Benign

0.0095

MetaRNN

Benign

0.15

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.9

.;M;M;M;.

MutationTaster

Benign

0.98

N;N;N

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-1.6

N;N;N;N;N

REVEL

Benign

0.067

Sift

Uncertain

0.016

D;D;D;D;D

Sift4G

Benign

0.12

T;T;T;T;D

Polyphen

0.90, 1.0

.;P;P;D;.

Vest4

0.22, 0.22, 0.20

MutPred

0.27

.;Gain of MoRF binding (P = 0.0392);Gain of MoRF binding (P = 0.0392);Gain of MoRF binding (P = 0.0392);.;

MVP

0.13

MPC

0.62

ClinPred

0.62

GERP RS

3.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.13

gMVP

0.11

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over