dbSNP rs998684043: MAP1S:p.Tyr32Cys (chr19-17719597-A-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018174.6(MAP1S):c.95A>G(p.Tyr32Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y32F) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MAP1S
NM_018174.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

Publications

0 publications found

Variant links:

Genes affected

MAP1S (HGNC:15715): (microtubule associated protein 1S) Enables DNA binding activity and cytoskeletal protein binding activity. Involved in microtubule bundle formation; neuron projection morphogenesis; and regulation of chromatin disassembly. Located in several cellular components, including microtubule cytoskeleton; nuclear lumen; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MAP1S links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.18654528).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP1S	NM_018174.6 link	c.95A>G	p.Tyr32Cys	missense_variant	Exon 1 of 7	ENST00000324096.9	NP_060644.4	Q66K74-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP1S	ENST00000324096.9 link	c.95A>G	p.Tyr32Cys	missense_variant	Exon 1 of 7	1	NM_018174.6	ENSP00000325313.3		Q66K74-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1091892

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

515430

African (AFR)

AF:

0.00

AC:

AN:

22858

American (AMR)

AF:

0.00

AC:

AN:

8352

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14244

East Asian (EAS)

AF:

0.00

AC:

AN:

26366

South Asian (SAS)

AF:

0.00

AC:

AN:

19512

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35254

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3304

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

918404

Other (OTH)

AF:

0.00

AC:

AN:

43598

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.034

T;.;.

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.022

LIST_S2

Benign

0.79

T;T;T

M_CAP

Uncertain

0.22

MetaRNN

Benign

0.19

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.2

L;.;.

PhyloP100

0.19

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

0.40

N;.;.

REVEL

Benign

0.11

Sift

Benign

0.20

T;.;.

Sift4G

Benign

0.18

T;T;T

Polyphen

1.0

D;.;.

Vest4

0.40

MutPred

0.35

Loss of stability (P = 0.1059);Loss of stability (P = 0.1059);Loss of stability (P = 0.1059);

MVP

0.25

MPC

1.1

ClinPred

0.31

GERP RS

-0.15

PromoterAI

-0.19

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.083

gMVP

0.39

Mutation Taster

=96/4

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over