rs4830513

Positions:

• chrX-13899714-G-A
• chrX-13899714-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+38793C>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 0.56 (13370 hom., 17542 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: GPM6B ENST00000454189.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPM6B	XM_047442007.1	c.-10751C>T		5_prime_UTR_variant	1/8		XP_047297963.1
GPM6B	NM_001001994.3	c.4+38793C>T		intron_variant			NP_001001994.1
GPM6B	NM_001318729.2	c.4+38793C>T		intron_variant			NP_001305658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.4+38793C>T		intron_variant		1		ENSP00000389915	A1
GPM6B	ENST00000398361.7	c.-198+38613C>T		intron_variant		2		ENSP00000381402

Frequencies

GnomAD3 genomes AF: 0.560 AC: 61092 AN: 109097 Hom.: 13366 Cov.: 21 AF XY: 0.557 AC XY: 17492 AN XY: 31397

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.549

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: 0.560 AC: 61147 AN: 109153 Hom.: 13370 Cov.: 21 AF XY: 0.558 AC XY: 17542 AN XY: 31463

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.555

Alfa AF: 0.505 Hom.: 3660

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4830513; hg19: chrX-13917833;