X-13785841-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001001995.3(GPM6B):​c.182-33G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.60 ( 13958 hom., 19562 hem., cov: 23)
Exomes 𝑓: 0.60 ( 123171 hom. 191233 hem. )
Failed GnomAD Quality Control

Consequence

GPM6B
NM_001001995.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.783
Variant links:
Genes affected
GPM6B (HGNC:4461): (glycoprotein M6B) This gene encodes a membrane glycoprotein that belongs to the proteolipid protein family. Proteolipid protein family members are expressed in most brain regions and are thought to be involved in cellular housekeeping functions such as membrane trafficking and cell-to-cell communication. This protein may also be involved in osteoblast differentiation. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are located on chromosomes Y and 22. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPM6BNM_001001995.3 linkc.182-33G>A intron_variant Intron 2 of 7 ENST00000316715.9 NP_001001995.1 Q13491-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPM6BENST00000316715.9 linkc.182-33G>A intron_variant Intron 2 of 7 2 NM_001001995.3 ENSP00000316861.4 Q13491-4

Frequencies

GnomAD3 genomes
AF:
0.599
AC:
66027
AN:
110261
Hom.:
13961
Cov.:
23
AF XY:
0.600
AC XY:
19517
AN XY:
32525
show subpopulations
Gnomad AFR
AF:
0.618
Gnomad AMI
AF:
0.515
Gnomad AMR
AF:
0.673
Gnomad ASJ
AF:
0.561
Gnomad EAS
AF:
0.549
Gnomad SAS
AF:
0.631
Gnomad FIN
AF:
0.600
Gnomad MID
AF:
0.526
Gnomad NFE
AF:
0.578
Gnomad OTH
AF:
0.598
GnomAD3 exomes
AF:
0.625
AC:
95747
AN:
153076
Hom.:
21738
AF XY:
0.632
AC XY:
27163
AN XY:
42962
show subpopulations
Gnomad AFR exome
AF:
0.620
Gnomad AMR exome
AF:
0.794
Gnomad ASJ exome
AF:
0.563
Gnomad EAS exome
AF:
0.559
Gnomad SAS exome
AF:
0.651
Gnomad FIN exome
AF:
0.608
Gnomad NFE exome
AF:
0.583
Gnomad OTH exome
AF:
0.618
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.598
AC:
611623
AN:
1022670
Hom.:
123171
Cov.:
19
AF XY:
0.634
AC XY:
191233
AN XY:
301412
show subpopulations
Gnomad4 AFR exome
AF:
0.620
Gnomad4 AMR exome
AF:
0.783
Gnomad4 ASJ exome
AF:
0.572
Gnomad4 EAS exome
AF:
0.552
Gnomad4 SAS exome
AF:
0.646
Gnomad4 FIN exome
AF:
0.605
Gnomad4 NFE exome
AF:
0.589
Gnomad4 OTH exome
AF:
0.592
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.599
AC:
66065
AN:
110316
Hom.:
13958
Cov.:
23
AF XY:
0.600
AC XY:
19562
AN XY:
32590
show subpopulations
Gnomad4 AFR
AF:
0.618
Gnomad4 AMR
AF:
0.674
Gnomad4 ASJ
AF:
0.561
Gnomad4 EAS
AF:
0.550
Gnomad4 SAS
AF:
0.633
Gnomad4 FIN
AF:
0.600
Gnomad4 NFE
AF:
0.578
Gnomad4 OTH
AF:
0.601
Alfa
AF:
0.517
Hom.:
6672
Bravo
AF:
0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.0040
DANN
Benign
0.43

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: rs5978663; hg19: chrX-13803960; API