X-13832666-C-T

Variant names:

• chrX-13832666-C-T
• rs11095629
• ENST00000454189.7:c.5-46858G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000454189.7(GPM6B):​c.5-46858G>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 0.74 (21006 hom., 24296 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: GPM6B ENST00000454189.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6B	NM_001318729.2	c.5-46858G>A		intron_variant	Intron 1 of 6		NP_001305658.1
GPM6B	NM_001001994.3	c.5-46858G>A		intron_variant	Intron 1 of 6		NP_001001994.1
GPM6B	XM_011545497.3	c.5-24897G>A		intron_variant	Intron 1 of 7		XP_011543799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.5-46858G>A		intron_variant	Intron 1 of 6	1		ENSP00000389915.2
GPM6B	ENST00000398361.7	c.-197-46858G>A		intron_variant	Intron 1 of 6	2		ENSP00000381402.3
GPM6B	ENST00000493085.5	c.-197-46858G>A		intron_variant	Intron 1 of 3	3		ENSP00000418199.1
GPM6B	ENST00000468080.1	c.-197-46858G>A		intron_variant	Intron 1 of 3	4		ENSP00000419779.1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 81331 AN: 110462 Hom.: 21002 Cov.: 23

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.719

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.736 AC: 81390 AN: 110515 Hom.: 21006 Cov.: 23 AF XY: 0.741 AC XY: 24296 AN XY: 32769

African (AFR) AF: 0.728 AC: 22122 AN: 30388

American (AMR) AF: 0.798 AC: 8234 AN: 10324

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 1964 AN: 2637

East Asian (EAS) AF: 0.757 AC: 2659 AN: 3511

South Asian (SAS) AF: 0.756 AC: 1991 AN: 2635

European-Finnish (FIN) AF: 0.793 AC: 4554 AN: 5745

Middle Eastern (MID) AF: 0.690 AC: 147 AN: 213

European-Non Finnish (NFE) AF: 0.722 AC: 38168 AN: 52886

Other (OTH) AF: 0.719 AC: 1085 AN: 1508

Alfa AF: 0.723 Hom.: 23078

Bravo AF: 0.739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11095629; hg19: chrX-13850785;