rs2449539

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018407.6(LAPTM4B):​c.603+9874T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0763 in 152,278 control chromosomes in the GnomAD database, including 998 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 0.076 ( 998 hom., cov: 33)

Consequence

LAPTM4B
NM_018407.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.23
Variant links:
Genes affected
LAPTM4B (HGNC:13646): (lysosomal protein transmembrane 4 beta) Enables ceramide binding activity; enzyme binding activity; and phosphatidylinositol bisphosphate binding activity. Involved in several processes, including negative regulation of macromolecule metabolic process; regulation of lysosomal membrane permeability; and regulation of lysosome organization. Located in several cellular components, including endosome; lysosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LAPTM4BNM_018407.6 linkuse as main transcriptc.603+9874T>C intron_variant ENST00000521545.7 NP_060877.4 Q86VI4-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LAPTM4BENST00000521545.7 linkuse as main transcriptc.603+9874T>C intron_variant 1 NM_018407.6 ENSP00000428409.1 Q86VI4-2
LAPTM4BENST00000445593.6 linkuse as main transcriptc.876+9874T>C intron_variant 1 ENSP00000402301.2 Q86VI4-3
LAPTM4BENST00000619747.1 linkuse as main transcriptc.876+9874T>C intron_variant 1 ENSP00000482533.1 Q86VI4-3

Frequencies

GnomAD3 genomes
AF:
0.0762
AC:
11599
AN:
152160
Hom.:
993
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0645
Gnomad AMI
AF:
0.0264
Gnomad AMR
AF:
0.183
Gnomad ASJ
AF:
0.0528
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.222
Gnomad FIN
AF:
0.0847
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.0270
Gnomad OTH
AF:
0.0941
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0763
AC:
11618
AN:
152278
Hom.:
998
Cov.:
33
AF XY:
0.0855
AC XY:
6366
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0645
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.0528
Gnomad4 EAS
AF:
0.366
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.0847
Gnomad4 NFE
AF:
0.0270
Gnomad4 OTH
AF:
0.0964
Alfa
AF:
0.0485
Hom.:
498
Bravo
AF:
0.0829
Asia WGS
AF:
0.271
AC:
938
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.23
DANN
Benign
0.61

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2449539; hg19: chr8-98847255; API