dbSNP rs9512: ABLIM3:c.*1795G>A (chr5-149260199-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014945.5(ABLIM3):c.*1795G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,690 control chromosomes in the GnomAD database, including 20,722 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 20621 hom., cov: 30)

Exomes 𝑓: 0.48 ( 101 hom. )

Consequence

ABLIM3
NM_014945.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.319

Publications

4 publications found

Variant links:

Genes affected

ABLIM3 (HGNC:29132): (actin binding LIM protein family member 3) This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]

ABLIM3 links:

ENSG00000253406 (HGNC:):

ENSG00000253406 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM3	NM_014945.5 link	c.*1795G>A		3_prime_UTR_variant	Exon 24 of 24	ENST00000309868.12	NP_055760.1	O94929-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM3	ENST00000309868.12 link	c.*1795G>A		3_prime_UTR_variant	Exon 24 of 24	1	NM_014945.5	ENSP00000310309.7		O94929-1

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

77840

AN:

151730

Hom.:

20593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.625

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.595

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.469

GnomAD4 exome

AF:

0.482

AC:

405

AN:

840

Hom.:

101

Cov.:

AF XY:

0.494

AC XY:

235

AN XY:

476

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.381

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.422

AC:

167

AN:

396

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.557

AC:

204

AN:

366

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.513

AC:

77915

AN:

151850

Hom.:

20621

Cov.:

AF XY:

0.503

AC XY:

37325

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.625

AC:

25872

AN:

41402

American (AMR)

AF:

0.418

AC:

6379

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1220

AN:

3466

East Asian (EAS)

AF:

0.594

AC:

3060

AN:

5148

South Asian (SAS)

AF:

0.463

AC:

2223

AN:

4806

European-Finnish (FIN)

AF:

0.388

AC:

4086

AN:

10518

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.496

AC:

33693

AN:

67938

Other (OTH)

AF:

0.471

AC:

989

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1858

3716

5575

7433

9291

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.495

Hom.:

11332

Bravo

AF:

0.520

Asia WGS

AF:

0.542

AC:

1888

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.37

(source)

DANN

Benign

0.68

PhyloP100

-0.32

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over