Genetic Variant ABI3BP:p.Arg1458Ser (chr3-100775295-C-A) – 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_001375547.2(ABI3BP):c.4374G>T(p.Arg1458Ser) 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ABI3BP
NM_001375547.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0960

Publications

0 publications found

Variant links:

Genes affected

ABI3BP (HGNC:17265): (ABI family member 3 binding protein) Predicted to enable actin filament binding activity and glycosaminoglycan binding activity. Predicted to be involved in regulation of actin cytoskeleton reorganization; regulation of dendritic spine morphogenesis; and regulation of postsynaptic density assembly. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in extracellular space. Colocalizes with collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ABI3BP 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=0.090403676).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375547.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ABI3BP	NM_001375547.2	MANE Select	c.4374G>T	p.Arg1458Ser	missense	Exon 60 of 68	NP_001362476.1	D3YTG3
ABI3BP	NM_001375550.1		c.4332G>T	p.Arg1444Ser	missense	Exon 59 of 67	NP_001362479.1
ABI3BP	NM_001375549.2		c.4326G>T	p.Arg1442Ser	missense	Exon 59 of 67	NP_001362478.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ABI3BP	ENST00000471714.6	TSL:5 MANE Select	c.4374G>T	p.Arg1458Ser	missense	Exon 60 of 68	ENSP00000420524.2	D3YTG3
ABI3BP	ENST00000284322.10	TSL:1	c.2220G>T	p.Arg740Ser	missense	Exon 27 of 35	ENSP00000284322.6	Q7Z7G0-1
ABI3BP	ENST00000470336.5	TSL:1	n.837G>T		non_coding_transcript_exon	Exon 10 of 18

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1456578

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

723906

African (AFR)

AF:

0.00

AC:

AN:

33424

American (AMR)

AF:

0.00

AC:

AN:

44042

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25990

East Asian (EAS)

AF:

0.00

AC:

AN:

39564

South Asian (SAS)

AF:

0.00

AC:

AN:

84998

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53198

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1109374

Other (OTH)

AF:

0.00

AC:

AN:

60222

GnomAD4 genome

Cov.:

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

0.21

BayesDel_addAF

Benign

-0.17

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.011

Eigen

Benign

-0.69

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.85

M_CAP

Benign

0.020

MetaRNN

Benign

0.090

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.9

PhyloP100

-0.096

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.2

REVEL

Benign

0.051

Sift

Benign

0.18

Sift4G

Benign

0.73

Polyphen

0.20

Vest4

0.37

MutPred

0.20

Loss of glycosylation at P1447 (P = 0.0205)

MVP

0.67

MPC

0.46

ClinPred

0.35

GERP RS

-1.2

Varity_R

0.077

gMVP

0.27

Mutation Taster

=99/1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over