X-13785841-C-T

Variant names:

• chrX-13785841-C-T
• rs5978663
• NM_001001995.3:c.182-33G>A

Variant summary

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

The NM_001001995.3(GPM6B):​c.182-33G>A 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 0.60 (13958 hom., 19562 hem., cov: 23)
  • Exomes 𝑓: 0.60 (123171 hom. 191233 hem.)
  • Failed GnomAD Quality Control
• Consequence: GPM6B NM_001001995.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6B	NM_001001995.3	c.182-33G>A		intron_variant	Intron 2 of 7	ENST00000316715.9	NP_001001995.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6B	ENST00000316715.9	c.182-33G>A		intron_variant	Intron 2 of 7	2	NM_001001995.3	ENSP00000316861.4

Frequencies

GnomAD3 genomes AF: 0.599 AC: 66027 AN: 110261 Hom.: 13961 Cov.: 23 AF XY: 0.600 AC XY: 19517 AN XY: 32525

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.598

GnomAD3 exomes AF: 0.625 AC: 95747 AN: 153076 Hom.: 21738 AF XY: 0.632 AC XY: 27163 AN XY: 42962

Gnomad AFR exome AF: 0.620

Gnomad AMR exome AF: 0.794

Gnomad ASJ exome AF: 0.563

Gnomad EAS exome AF: 0.559

Gnomad SAS exome AF: 0.651

Gnomad FIN exome AF: 0.608

Gnomad NFE exome AF: 0.583

Gnomad OTH exome AF: 0.618

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.598 AC: 611623 AN: 1022670 Hom.: 123171 Cov.: 19 AF XY: 0.634 AC XY: 191233 AN XY: 301412

Gnomad4 AFR exome AF: 0.620

Gnomad4 AMR exome AF: 0.783

Gnomad4 ASJ exome AF: 0.572

Gnomad4 EAS exome AF: 0.552

Gnomad4 SAS exome AF: 0.646

Gnomad4 FIN exome AF: 0.605

Gnomad4 NFE exome AF: 0.589

Gnomad4 OTH exome AF: 0.592

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.599 AC: 66065 AN: 110316 Hom.: 13958 Cov.: 23 AF XY: 0.600 AC XY: 19562 AN XY: 32590

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.601

Alfa AF: 0.517 Hom.: 6672

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0040
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5978663; hg19: chrX-13803960;