rs13144140

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.132
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
GPM6ANM_201591.3 linkuse as main transcriptc.38-43268C>T intron_variant ENST00000393658.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPM6AENST00000393658.7 linkuse as main transcriptc.38-43268C>T intron_variant 1 NM_201591.3 P1P51674-1

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33035
AN:
151714
Hom.:
3863
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.150
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.211
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.116
Gnomad4 FIN
AF:
0.304
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.229
Alfa
AF:
0.241
Hom.:
5849
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13144140; hg19: chr4-176666186; API