Variant X-13892190-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000454189.7(GPM6B):c.4+46317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 111,064 control chromosomes in the GnomAD database, including 1,979 homozygotes. There are 6,678 hemizygotes in GnomAD. 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 ( 1979 hom., 6678 hem., cov: 22)

Consequence

GPM6B
ENST00000454189.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.672

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]

GPM6B links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
GPM6B	XM_047442007.1 linkuse as main transcript	c.-3227T>C	5_prime_UTR_variant	1/8
GPM6B	NM_001001994.3 linkuse as main transcript	c.4+46317T>C	intron_variant
GPM6B	NM_001318729.2 linkuse as main transcript	c.4+46317T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPM6B	ENST00000454189.7 linkuse as main transcript	c.4+46317T>C		intron_variant		1		A1	Q13491-2
GPM6B	ENST00000398361.7 linkuse as main transcript	c.-198+46137T>C		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

23164

AN:

111007

Hom.:

1981

Cov.:

AF XY:

0.200

AC XY:

6654

AN XY:

33227

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.0424

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.148

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.188

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.209

AC:

23183

AN:

111064

Hom.:

1979

Cov.:

AF XY:

0.201

AC XY:

6678

AN XY:

33294

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.343

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.191

Alfa

AF:

0.187

Hom.:

4178

Bravo

AF:

0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.1

DANN

Benign

0.26

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over