Genetic Variant PDLIM1:c.*203T>G (chr10-95237722-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020992.4(PDLIM1):c.*203T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 567,644 control chromosomes in the GnomAD database, including 144,082 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 0.64 ( 33639 hom., cov: 33)

Exomes 𝑓: 0.71 ( 110443 hom. )

Consequence

PDLIM1
NM_020992.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.172

Publications

9 publications found

Variant links:

Genes affected

PDLIM1 (HGNC:2067): (PDZ and LIM domain 1) This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]

PDLIM1 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDLIM1	NM_020992.4 link	c.*203T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000329399.7	NP_066272.1	O00151V9HW92

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDLIM1	ENST00000329399.7 link	c.*203T>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_020992.4	ENSP00000360305.3		O00151
PDLIM1	ENST00000492511.1 link	n.*218T>G		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.637

AC:

96886

AN:

151994

Hom.:

33621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.791

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.678

Gnomad FIN

AF:

0.724

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.787

Gnomad OTH

AF:

0.680

GnomAD4 exome

AF:

0.708

AC:

294059

AN:

415532

Hom.:

110443

Cov.:

AF XY:

0.711

AC XY:

154044

AN XY:

216710

show subpopulations

African (AFR)

AF:

0.394

AC:

4683

AN:

11876

American (AMR)

AF:

0.658

AC:

11227

AN:

17070

Ashkenazi Jewish (ASJ)

AF:

0.726

AC:

9474

AN:

13042

East Asian (EAS)

AF:

0.151

AC:

4463

AN:

29648

South Asian (SAS)

AF:

0.701

AC:

26268

AN:

37468

European-Finnish (FIN)

AF:

0.736

AC:

20577

AN:

27944

Middle Eastern (MID)

AF:

0.739

AC:

1382

AN:

1870

European-Non Finnish (NFE)

AF:

0.788

AC:

198760

AN:

252088

Other (OTH)

AF:

0.702

AC:

17225

AN:

24526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

3400

6800

10201

13601

17001

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.637

AC:

96945

AN:

152112

Hom.:

33639

Cov.:

AF XY:

0.635

AC XY:

47241

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.397

AC:

16455

AN:

41468

American (AMR)

AF:

0.677

AC:

10347

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.731

AC:

2537

AN:

3470

East Asian (EAS)

AF:

0.154

AC:

799

AN:

5184

South Asian (SAS)

AF:

0.680

AC:

3270

AN:

4812

European-Finnish (FIN)

AF:

0.724

AC:

7649

AN:

10572

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.787

AC:

53515

AN:

68002

Other (OTH)

AF:

0.677

AC:

1428

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1540

3080

4619

6159

7699

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.713

Hom.:

19412

Bravo

AF:

0.618

Asia WGS

AF:

0.440

AC:

1533

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.1

(source)

DANN

Benign

0.58

PhyloP100

0.17

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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