4-175742719-A-G

Variant names:

• chr4-175742719-A-G
• rs10520306
• NM_201591.3:c.38-40952T>C

Variant summary

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

The NM_201591.3(GPM6A):​c.38-40952T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,232 control chromosomes in the GnomAD database, including 377 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 0.053 (377 hom., cov: 32)
• Consequence: GPM6A NM_201591.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201591.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPM6A	NM_201591.3	MANE Select	c.38-40952T>C		intron	N/A	NP_963885.1
	GPM6A	NM_005277.5		c.38-40952T>C		intron	N/A	NP_005268.1
	GPM6A	NM_001261448.2		c.17-40952T>C		intron	N/A	NP_001248377.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPM6A	ENST00000393658.7	TSL:1 MANE Select	c.38-40952T>C		intron	N/A	ENSP00000377268.2
	GPM6A	ENST00000280187.11	TSL:1	c.38-40952T>C		intron	N/A	ENSP00000280187.7
	GPM6A	ENST00000506894.5	TSL:1	c.5-40952T>C		intron	N/A	ENSP00000421578.1

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8080 AN: 152114 Hom.: 376 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0531 AC: 8090 AN: 152232 Hom.: 377 Cov.: 32 AF XY: 0.0574 AC XY: 4275 AN XY: 74426

African (AFR) AF: 0.0514 AC: 2135 AN: 41554

American (AMR) AF: 0.0664 AC: 1014 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5160

South Asian (SAS) AF: 0.0827 AC: 399 AN: 4826

European-Finnish (FIN) AF: 0.0577 AC: 612 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2199 AN: 68030

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0176 Hom.: 12

Bravo AF: 0.0554

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.58
PhyloP100		0.45
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: rs10520306; hg19: chr4-176663870;