rs4830513

Variant names:

• chrX-13899714-G-A
• rs4830513
• ENST00000454189.7:c.4+38793C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-13899714-G-A
• chrX-13899714-G-T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 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=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6B	XM_047442007.1	c.-10751C>T		5_prime_UTR_variant	Exon 1 of 8		XP_047297963.1
GPM6B	NM_001318729.2	c.4+38793C>T		intron_variant	Intron 1 of 6		NP_001305658.1
GPM6B	NM_001001994.3	c.4+38793C>T		intron_variant	Intron 1 of 6		NP_001001994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.4+38793C>T		intron_variant	Intron 1 of 6	1		ENSP00000389915.2
GPM6B	ENST00000398361.7	c.-198+38613C>T		intron_variant	Intron 1 of 6	2		ENSP00000381402.3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 61092 AN: 109097 Hom.: 13366 Cov.: 21

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

African (AFR) AF: 0.749 AC: 22380 AN: 29862

American (AMR) AF: 0.671 AC: 6839 AN: 10188

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1250 AN: 2621

East Asian (EAS) AF: 0.923 AC: 3160 AN: 3423

South Asian (SAS) AF: 0.735 AC: 1848 AN: 2514

European-Finnish (FIN) AF: 0.434 AC: 2457 AN: 5661

Middle Eastern (MID) AF: 0.481 AC: 104 AN: 216

European-Non Finnish (NFE) AF: 0.422 AC: 22144 AN: 52514

Other (OTH) AF: 0.555 AC: 822 AN: 1481

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
PhyloP100		0.037
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: rs4830513; hg19: chrX-13917833;