Genetic Variant LAPTM5:p.Ser40Ser (chr1-30742517-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006762.3(LAPTM5):c.120A>G(p.Ser40Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,612,044 control chromosomes in the GnomAD database, including 217,685 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 0.55 ( 23304 hom., cov: 32)

Exomes 𝑓: 0.51 ( 194381 hom. )

Consequence

LAPTM5
NM_006762.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.21

Publications

21 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP7

Synonymous conserved (PhyloP=-5.21 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAPTM5	NM_006762.3 link	c.120A>G	p.Ser40Ser	synonymous_variant	Exon 2 of 8	ENST00000294507.4	NP_006753.1	Q13571Q5TBB8
LAPTM5	XM_011542098.3 link	c.88-2580A>G		intron_variant	Intron 1 of 5		XP_011540400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LAPTM5	ENST00000294507.4 link	c.120A>G	p.Ser40Ser	synonymous_variant	Exon 2 of 8	1	NM_006762.3	ENSP00000294507.3	Q13571
LAPTM5	ENST00000464569.1 link	n.345A>G		non_coding_transcript_exon_variant	Exon 2 of 8	5
LAPTM5	ENST00000476492.1 link	n.132A>G		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

83528

AN:

151942

Hom.:

23273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.600

Gnomad AMI

AF:

0.470

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.480

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.584

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.542

GnomAD2 exomes

AF:

0.556

AC:

138954

AN:

249732

AF XY:

0.547

show subpopulations

Gnomad AFR exome

AF:

0.603

Gnomad AMR exome

AF:

0.729

Gnomad ASJ exome

AF:

0.483

Gnomad EAS exome

AF:

0.693

Gnomad FIN exome

AF:

0.583

Gnomad NFE exome

AF:

0.483

Gnomad OTH exome

AF:

0.527

GnomAD4 exome

AF:

0.511

AC:

746647

AN:

1459984

Hom.:

194381

Cov.:

AF XY:

0.511

AC XY:

371022

AN XY:

726274

show subpopulations

African (AFR)

AF:

0.602

AC:

20161

AN:

33468

American (AMR)

AF:

0.719

AC:

32114

AN:

44636

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

12494

AN:

26110

East Asian (EAS)

AF:

0.722

AC:

28639

AN:

39668

South Asian (SAS)

AF:

0.539

AC:

46433

AN:

86140

European-Finnish (FIN)

AF:

0.569

AC:

30180

AN:

53080

Middle Eastern (MID)

AF:

0.528

AC:

3047

AN:

5768

European-Non Finnish (NFE)

AF:

0.488

AC:

542018

AN:

1110764

Other (OTH)

AF:

0.523

AC:

31561

AN:

60350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

17515

35031

52546

70062

87577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.550

AC:

83607

AN:

152060

Hom.:

23304

Cov.:

AF XY:

0.555

AC XY:

41272

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.600

AC:

24878

AN:

41448

American (AMR)

AF:

0.647

AC:

9888

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

1661

AN:

3464

East Asian (EAS)

AF:

0.683

AC:

3535

AN:

5172

South Asian (SAS)

AF:

0.528

AC:

2547

AN:

4822

European-Finnish (FIN)

AF:

0.584

AC:

6186

AN:

10592

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33182

AN:

67956

Other (OTH)

AF:

0.546

AC:

1152

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1943

3886

5829

7772

9715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.511

Hom.:

41744

Bravo

AF:

0.561

Asia WGS

AF:

0.620

AC:

2155

AN:

3478

EpiCase

AF:

0.488

EpiControl

AF:

0.487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.17

(source)

DANN

Benign

0.36

PhyloP100

-5.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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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1-30742517-T-C

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