rs1188349

Variant summary

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

The NM_006762.3(LAPTM5):​c.87+6849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,174 control chromosomes in the GnomAD database, including 3,799 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 0.21 ( 3799 hom., cov: 33)

Consequence

LAPTM5
NM_006762.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.432
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LAPTM5NM_006762.3 linkuse as main transcriptc.87+6849C>T intron_variant ENST00000294507.4
LOC105378620XR_007065566.1 linkuse as main transcriptn.1551C>T non_coding_transcript_exon_variant 1/2
LAPTM5XM_011542098.3 linkuse as main transcriptc.87+6849C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LAPTM5ENST00000294507.4 linkuse as main transcriptc.87+6849C>T intron_variant 1 NM_006762.3 P1
LAPTM5ENST00000476492.1 linkuse as main transcriptn.99+6849C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
32116
AN:
152056
Hom.:
3797
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.229
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.244
Gnomad EAS
AF:
0.276
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.199
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.271
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32126
AN:
152174
Hom.:
3799
Cov.:
33
AF XY:
0.208
AC XY:
15502
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.244
Gnomad4 EAS
AF:
0.278
Gnomad4 SAS
AF:
0.282
Gnomad4 FIN
AF:
0.199
Gnomad4 NFE
AF:
0.271
Gnomad4 OTH
AF:
0.208
Alfa
AF:
0.188
Hom.:
995
Bravo
AF:
0.204
Asia WGS
AF:
0.249
AC:
871
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
8.7
DANN
Benign
0.77

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: rs1188349; hg19: chr1-31223657; COSMIC: COSV53852850; COSMIC: COSV53852850; API