rs1005589

Variant names:

• chrX-13873228-G-A
• rs1005589
• ENST00000454189.7:c.4+65279C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-13873228-G-A
• chrX-13873228-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+65279C>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 0.75 (22883 hom., 23105 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: GPM6B ENST00000454189.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• 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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6B	NM_001318729.2	c.4+65279C>T		intron_variant	Intron 1 of 6		NP_001305658.1
GPM6B	NM_001001994.3	c.4+65279C>T		intron_variant	Intron 1 of 6		NP_001001994.1
GPM6B	XM_011545497.3	c.4+65279C>T		intron_variant	Intron 1 of 7		XP_011543799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000454189.7	c.4+65279C>T		intron_variant	Intron 1 of 6	1		ENSP00000389915.2
GPM6B	ENST00000398361.7	c.-198+65099C>T		intron_variant	Intron 1 of 6	2		ENSP00000381402.3
GPM6B	ENST00000493085.5	c.-198+15753C>T		intron_variant	Intron 1 of 3	3		ENSP00000418199.1
GPM6B	ENST00000468080.1	c.-198+16224C>T		intron_variant	Intron 1 of 3	4		ENSP00000419779.1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 81744 AN: 108248 Hom.: 22885 Cov.: 21

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.788

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: 0.755 AC: 81758 AN: 108295 Hom.: 22883 Cov.: 21 AF XY: 0.754 AC XY: 23105 AN XY: 30663

African (AFR) AF: 0.541 AC: 16101 AN: 29785

American (AMR) AF: 0.775 AC: 7798 AN: 10057

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2146 AN: 2616

East Asian (EAS) AF: 0.927 AC: 3180 AN: 3432

South Asian (SAS) AF: 0.835 AC: 2022 AN: 2422

European-Finnish (FIN) AF: 0.834 AC: 4465 AN: 5355

Middle Eastern (MID) AF: 0.837 AC: 180 AN: 215

European-Non Finnish (NFE) AF: 0.844 AC: 44115 AN: 52284

Other (OTH) AF: 0.789 AC: 1148 AN: 1455

Alfa AF: 0.810 Hom.: 74095

Bravo AF: 0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.37
PhyloP100		-0.55
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: rs1005589; hg19: chrX-13891347;