chrX-13915914-G-A

Variant names:

• chrX-13915914-G-A
• rs5979998
• ENST00000454189.7:c.4+22593C>T

Variant summary

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

The NM_001318729.2(GPM6B):​c.4+22593C>T 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 0.68 (18835 hom., 22011 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: GPM6B NM_001318729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 2 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=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318729.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPM6B	NM_001318729.2		c.4+22593C>T		intron	N/A	NP_001305658.1
	GPM6B	NM_001001994.3		c.4+22593C>T		intron	N/A	NP_001001994.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPM6B	ENST00000454189.7	TSL:1	c.4+22593C>T		intron	N/A	ENSP00000389915.2
	GPM6B	ENST00000398361.7	TSL:2	c.-198+22413C>T		intron	N/A	ENSP00000381402.3

Frequencies

GnomAD3 genomes AF: 0.685 AC: 75617 AN: 110429 Hom.: 18842 Cov.: 23

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.659

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: 0.685 AC: 75655 AN: 110480 Hom.: 18835 Cov.: 23 AF XY: 0.673 AC XY: 22011 AN XY: 32728

African (AFR) AF: 0.701 AC: 21285 AN: 30359

American (AMR) AF: 0.556 AC: 5771 AN: 10385

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 1895 AN: 2625

East Asian (EAS) AF: 0.332 AC: 1164 AN: 3501

South Asian (SAS) AF: 0.494 AC: 1287 AN: 2605

European-Finnish (FIN) AF: 0.719 AC: 4158 AN: 5783

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

European-Non Finnish (NFE) AF: 0.727 AC: 38420 AN: 52830

Other (OTH) AF: 0.656 AC: 987 AN: 1504

Alfa AF: 0.699 Hom.: 7692

Bravo AF: 0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.45
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: rs5979998; hg19: chrX-13934033;