Genetic Variant LAPTM5:c.*38G>A (chr1-30733790-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006762.3(LAPTM5):c.*38G>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 0.232 in 1,589,694 control chromosomes in the GnomAD database, including 46,042 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 0.18 ( 3061 hom., cov: 33)

Exomes 𝑓: 0.24 ( 42981 hom. )

Consequence

LAPTM5
NM_006762.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.760

Publications

15 publications found

Variant links:

Genes affected

LAPTM5 (HGNC:29612): (lysosomal protein transmembrane 5) This gene encodes a transmembrane receptor that is associated with lysosomes. The encoded protein, also known as E3 protein, may play a role in hematopoiesis. [provided by RefSeq, Feb 2009]

LAPTM5 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=-0.55).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAPTM5	NM_006762.3 link	c.*38G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000294507.4	NP_006753.1	Q13571Q5TBB8
LAPTM5	XM_011542098.3 link	c.*38G>A		3_prime_UTR_variant	Exon 6 of 6		XP_011540400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAPTM5	ENST00000294507.4 link	c.*38G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_006762.3	ENSP00000294507.3		Q13571
LAPTM5	ENST00000464569.1 link	n.*99G>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26710

AN:

152120

Hom.:

3067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0460

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.0697

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.172

GnomAD2 exomes

AF:

0.197

AC:

43294

AN:

220200

AF XY:

0.200

show subpopulations

Gnomad AFR exome

AF:

0.0411

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.210

Gnomad EAS exome

AF:

0.0808

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.258

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.237

AC:

341330

AN:

1437456

Hom.:

42981

Cov.:

AF XY:

0.235

AC XY:

168019

AN XY:

713682

show subpopulations

African (AFR)

AF:

0.0392

AC:

1271

AN:

32386

American (AMR)

AF:

0.108

AC:

4299

AN:

39818

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

5125

AN:

25324

East Asian (EAS)

AF:

0.0819

AC:

3211

AN:

39226

South Asian (SAS)

AF:

0.151

AC:

12627

AN:

83852

European-Finnish (FIN)

AF:

0.287

AC:

14224

AN:

49534

Middle Eastern (MID)

AF:

0.179

AC:

1010

AN:

5632

European-Non Finnish (NFE)

AF:

0.260

AC:

286991

AN:

1102418

Other (OTH)

AF:

0.212

AC:

12572

AN:

59266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

13051

26101

39152

52202

65253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9468

18936

28404

37872

47340

<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:

0.175

AC:

26702

AN:

152238

Hom.:

3061

Cov.:

AF XY:

0.173

AC XY:

12876

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0459

AC:

1908

AN:

41562

American (AMR)

AF:

0.135

AC:

2071

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

704

AN:

3468

East Asian (EAS)

AF:

0.0699

AC:

362

AN:

5182

South Asian (SAS)

AF:

0.126

AC:

606

AN:

4814

European-Finnish (FIN)

AF:

0.294

AC:

3110

AN:

10592

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.254

AC:

17303

AN:

68000

Other (OTH)

AF:

0.170

AC:

360

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1077

2155

3232

4310

5387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.226

Hom.:

7193

Bravo

AF:

0.159

Asia WGS

AF:

0.0860

AC:

298

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.76

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