rs1826763

Positions:

• chr4-175882901-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000280187.11(GPM6A):​c.-22-70652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,736 control chromosomes in the GnomAD database, including 25,560 homozygotes. 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 (25560 hom., cov: 32)
• Consequence: GPM6A ENST00000280187.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

GPM6A (HGNC:4460): (glycoprotein M6A) Predicted to enable calcium channel activity. Involved in neuron migration and stem cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPM6A	NM_001261447.1	c.282+119408G>A		intron_variant
GPM6A	NM_001388090.1	c.-153+8562G>A		intron_variant
GPM6A	NM_005277.5	c.-22-70652G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPM6A	ENST00000280187.11	c.-22-70652G>A		intron_variant		1		P1
GPM6A	ENST00000506894.5	c.4+119408G>A		intron_variant		1
GPM6A	ENST00000502754.5	c.-153+88976G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87820 AN: 151618 Hom.: 25558 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.579 AC: 87850 AN: 151736 Hom.: 25560 Cov.: 32 AF XY: 0.579 AC XY: 42931 AN XY: 74118

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.579

Alfa AF: 0.587 Hom.: 45227

Bravo AF: 0.584

Asia WGS AF: 0.571 AC: 1982 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.22

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: rs1826763; hg19: chr4-176804052;