rs13144140

Variant names:

• chr4-175745035-G-A
• rs13144140
• NM_201591.3:c.38-43268C>T

Variant summary

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

The NM_201591.3(GPM6A):​c.38-43268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,832 control chromosomes in the GnomAD database, including 3,866 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 0.22 (3866 hom., cov: 32)
• Consequence: GPM6A NM_201591.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPM6A	NM_201591.3	c.38-43268C>T		intron_variant	Intron 1 of 6	ENST00000393658.7	NP_963885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPM6A	ENST00000393658.7	c.38-43268C>T		intron_variant	Intron 1 of 6	1	NM_201591.3	ENSP00000377268.2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33035 AN: 151714 Hom.: 3863 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.218 AC: 33053 AN: 151832 Hom.: 3866 Cov.: 32 AF XY: 0.219 AC XY: 16254 AN XY: 74180

African (AFR) AF: 0.150 AC: 6213 AN: 41418

American (AMR) AF: 0.208 AC: 3170 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1324 AN: 5154

South Asian (SAS) AF: 0.116 AC: 561 AN: 4822

European-Finnish (FIN) AF: 0.304 AC: 3191 AN: 10502

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17180 AN: 67914

Other (OTH) AF: 0.229 AC: 482 AN: 2108

Alfa AF: 0.241 Hom.: 6772

Bravo AF: 0.208

Asia WGS AF: 0.180 AC: 625 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		0.13
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: rs13144140; hg19: chr4-176666186;