rs10520302

Variant names:

• chr4-175686888-C-T
• rs10520302
• NM_201591.3:c.231-13052G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201591.3(GPM6A):​c.231-13052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 152,248 control chromosomes in the GnomAD database, including 571 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 0.059 (571 hom., cov: 32)
• Consequence: GPM6A NM_201591.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6A	NM_201591.3	c.231-13052G>A		intron_variant	Intron 2 of 6	ENST00000393658.7	NP_963885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6A	ENST00000393658.7	c.231-13052G>A		intron_variant	Intron 2 of 6	1	NM_201591.3	ENSP00000377268.2

Frequencies

GnomAD3 genomes AF: 0.0585 AC: 8904 AN: 152130 Hom.: 573 Cov.: 32

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0585 AC: 8909 AN: 152248 Hom.: 571 Cov.: 32 AF XY: 0.0630 AC XY: 4688 AN XY: 74446

African (AFR) AF: 0.0114 AC: 472 AN: 41560

American (AMR) AF: 0.0785 AC: 1200 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0809 AC: 281 AN: 3472

East Asian (EAS) AF: 0.352 AC: 1823 AN: 5172

South Asian (SAS) AF: 0.128 AC: 619 AN: 4826

European-Finnish (FIN) AF: 0.0726 AC: 768 AN: 10584

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0530 AC: 3604 AN: 68020

Other (OTH) AF: 0.0535 AC: 113 AN: 2112

Alfa AF: 0.0558 Hom.: 983

Bravo AF: 0.0569

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10520302; hg19: chr4-176608039;