rs7890737

Positions:

• chrX-13898835-G-A
• chrX-13898835-G-C
• chrX-13898835-G-T

Variant summary

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

The ENST00000454189.7(GPM6B):​c.4+39672C>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 0.58 (14271 hom., 18904 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: GPM6B ENST00000454189.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPM6B	XM_047442007.1	c.-9872C>T		5_prime_UTR_variant	1/8		XP_047297963.1
GPM6B	NM_001001994.3	c.4+39672C>T		intron_variant			NP_001001994.1
GPM6B	NM_001318729.2	c.4+39672C>T		intron_variant			NP_001305658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.4+39672C>T		intron_variant		1		ENSP00000389915	A1
GPM6B	ENST00000398361.7	c.-198+39492C>T		intron_variant		2		ENSP00000381402

Frequencies

GnomAD3 genomes AF: 0.577 AC: 63654 AN: 110251 Hom.: 14264 Cov.: 22 AF XY: 0.580 AC XY: 18855 AN XY: 32499

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.489

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.561

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: 0.578 AC: 63710 AN: 110301 Hom.: 14271 Cov.: 22 AF XY: 0.581 AC XY: 18904 AN XY: 32559

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.566

Alfa AF: 0.385 Hom.: 2018

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7890737; hg19: chrX-13916954;