chr5-151252773-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000523466.5(GM2A):​c.127-6982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 213,782 control chromosomes in the GnomAD database, including 462 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.068 ( 343 hom., cov: 26)
Exomes 𝑓: 0.039 ( 119 hom. )

Consequence

GM2A
ENST00000523466.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.528
Variant links:
Genes affected
GM2A (HGNC:4367): (ganglioside GM2 activator) This gene encodes a small glycolipid transport protein which acts as a substrate specific co-factor for the lysosomal enzyme beta-hexosaminidase A. Beta-hexosaminidase A, together with GM2 ganglioside activator, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Mutations in this gene result in GM2-gangliosidosis type AB or the AB variant of Tay-Sachs disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 5-151252773-C-T is Benign according to our data. Variant chr5-151252773-C-T is described in ClinVar as [Benign]. Clinvar id is 1267493.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GM2AENST00000523466.5 linkuse as main transcriptc.127-6982C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0682
AC:
10225
AN:
149928
Hom.:
344
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.0800
Gnomad AMI
AF:
0.113
Gnomad AMR
AF:
0.0426
Gnomad ASJ
AF:
0.0930
Gnomad EAS
AF:
0.0767
Gnomad SAS
AF:
0.0863
Gnomad FIN
AF:
0.0495
Gnomad MID
AF:
0.150
Gnomad NFE
AF:
0.0657
Gnomad OTH
AF:
0.0654
GnomAD4 exome
AF:
0.0390
AC:
2489
AN:
63752
Hom.:
119
AF XY:
0.0402
AC XY:
1368
AN XY:
34000
show subpopulations
Gnomad4 AFR exome
AF:
0.0381
Gnomad4 AMR exome
AF:
0.0218
Gnomad4 ASJ exome
AF:
0.0489
Gnomad4 EAS exome
AF:
0.0522
Gnomad4 SAS exome
AF:
0.0571
Gnomad4 FIN exome
AF:
0.0242
Gnomad4 NFE exome
AF:
0.0355
Gnomad4 OTH exome
AF:
0.0394
GnomAD4 genome
AF:
0.0681
AC:
10220
AN:
150030
Hom.:
343
Cov.:
26
AF XY:
0.0673
AC XY:
4930
AN XY:
73200
show subpopulations
Gnomad4 AFR
AF:
0.0799
Gnomad4 AMR
AF:
0.0424
Gnomad4 ASJ
AF:
0.0930
Gnomad4 EAS
AF:
0.0761
Gnomad4 SAS
AF:
0.0860
Gnomad4 FIN
AF:
0.0495
Gnomad4 NFE
AF:
0.0657
Gnomad4 OTH
AF:
0.0642
Alfa
AF:
0.0662
Hom.:
40
Asia WGS
AF:
0.0820
AC:
286
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 21, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.7
DANN
Benign
0.78

Splicing

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: rs116594022; hg19: chr5-150632334; API