X-13928837-T-C

Variant names:

• chrX-13928837-T-C
• rs952076
• ENST00000454189.7:c.4+9670A>G

Variant summary

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

The ENST00000454189.7(GPM6B):​c.4+9670A>G 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 0.69 (19118 hom., 22268 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: GPM6B ENST00000454189.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• 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=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6B	NM_001318729.2	c.4+9670A>G		intron_variant	Intron 1 of 6		NP_001305658.1
GPM6B	NM_001001994.3	c.4+9670A>G		intron_variant	Intron 1 of 6		NP_001001994.1
GPM6B	XM_011545497.3	c.4+9670A>G		intron_variant	Intron 1 of 7		XP_011543799.1
GPM6B	XM_017029432.2	c.4+9670A>G		intron_variant	Intron 1 of 7		XP_016884921.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.4+9670A>G		intron_variant	Intron 1 of 6	1		ENSP00000389915.2
GPM6B	ENST00000398361.7	c.-198+9490A>G		intron_variant	Intron 1 of 6	2		ENSP00000381402.3

Frequencies

GnomAD3 genomes AF: 0.688 AC: 76248 AN: 110746 Hom.: 19124 Cov.: 23

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.666

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: 0.689 AC: 76292 AN: 110800 Hom.: 19118 Cov.: 23 AF XY: 0.674 AC XY: 22268 AN XY: 33036

African (AFR) AF: 0.721 AC: 21964 AN: 30451

American (AMR) AF: 0.561 AC: 5847 AN: 10424

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 1904 AN: 2638

East Asian (EAS) AF: 0.328 AC: 1148 AN: 3501

South Asian (SAS) AF: 0.446 AC: 1168 AN: 2616

European-Finnish (FIN) AF: 0.714 AC: 4170 AN: 5842

Middle Eastern (MID) AF: 0.650 AC: 139 AN: 214

European-Non Finnish (NFE) AF: 0.726 AC: 38400 AN: 52927

Other (OTH) AF: 0.663 AC: 998 AN: 1506

Alfa AF: 0.698 Hom.: 21533

Bravo AF: 0.676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		0.62
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: rs952076; hg19: chrX-13946956;