Genetic Variant NM_001168465.2:c.2155A>G (chrX-20010970-T-C) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001168465.2(MAP7D2):c.2155A>G(p.Asn719Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000898 in 111,312 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., 1 hem., cov: 23)

Consequence

MAP7D2
NM_001168465.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.02

Publications

0 publications found

Variant links:

Genes affected

MAP7D2 (HGNC:25899): (MAP7 domain containing 2) Predicted to be involved in microtubule cytoskeleton organization. Predicted to be active in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

MAP7D2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.37347317).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001168465.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MAP7D2	NM_001168465.2	MANE Select	c.2155A>G	p.Asn719Asp	missense	Exon 16 of 17	NP_001161937.1	Q96T17-2
MAP7D2	NM_152780.4		c.2032A>G	p.Asn678Asp	missense	Exon 15 of 16	NP_689993.2	Q96T17-1
MAP7D2	NM_001168466.2		c.1897A>G	p.Asn633Asp	missense	Exon 14 of 15	NP_001161938.1	Q96T17-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MAP7D2	ENST00000379643.10	TSL:1 MANE Select	c.2155A>G	p.Asn719Asp	missense	Exon 16 of 17	ENSP00000368964.5	Q96T17-2
MAP7D2	ENST00000379651.7	TSL:1	c.2032A>G	p.Asn678Asp	missense	Exon 15 of 16	ENSP00000368972.3	Q96T17-1
MAP7D2	ENST00000970014.1		c.2230A>G	p.Asn744Asp	missense	Exon 17 of 18	ENSP00000640074.1

Frequencies

GnomAD3 genomes

AF:

0.00000898

AC:

AN:

111312

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000898

AC:

AN:

111312

Hom.:

Cov.:

AF XY:

0.0000299

AC XY:

AN XY:

33492

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30542

American (AMR)

AF:

0.00

AC:

AN:

10443

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2642

East Asian (EAS)

AF:

0.00

AC:

AN:

3567

South Asian (SAS)

AF:

0.00

AC:

AN:

2628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5972

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000188

AC:

AN:

53094

Other (OTH)

AF:

0.00

AC:

AN:

1504

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.021

BayesDel_noAF

Benign

-0.27

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.39

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.88

M_CAP

Pathogenic

0.63

MetaRNN

Benign

0.37

MetaSVM

Uncertain

0.65

MutationAssessor

Benign

0.97

PhyloP100

5.0

PrimateAI

Uncertain

0.69

PROVEAN

Uncertain

-2.9

REVEL

Uncertain

0.44

Sift

Uncertain

0.0090

Sift4G

Benign

0.075

Polyphen

1.0

Vest4

0.16

MutPred

0.18

Loss of sheet (P = 0.0126)

MVP

0.83

MPC

0.14

ClinPred

0.97

GERP RS

5.4

Varity_R

0.74

gMVP

0.64

Mutation Taster

=63/37

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over