Genetic Variant 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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014945.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ABLIM3	NM_014945.5	MANE Select	c.*1795G>A	3_prime_UTR	Exon 24 of 24	NP_055760.1
ABLIM3	NM_001301015.3		c.*1795G>A	3_prime_UTR	Exon 23 of 23	NP_001287944.1
ABLIM3	NM_001301018.3		c.*1795G>A	3_prime_UTR	Exon 23 of 23	NP_001287947.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ABLIM3	ENST00000309868.12	TSL:1 MANE Select	c.*1795G>A	3_prime_UTR	Exon 24 of 24	ENSP00000310309.7
ABLIM3	ENST00000506113.5	TSL:1	c.*1795G>A	3_prime_UTR	Exon 23 of 23	ENSP00000425394.1
ABLIM3	ENST00000504238.5	TSL:1	c.*624G>A	3_prime_UTR	Exon 19 of 19	ENSP00000421183.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over