16-23505353-C-T

Variant summary

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

The NM_015044.4(GGA2):​c.91+4968G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,118 control chromosomes in the GnomAD database, including 579 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 0.046 ( 579 hom., cov: 32)

Consequence

GGA2
NM_015044.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01
Variant links:
Genes affected
GGA2 (HGNC:16064): (golgi associated, gamma adaptin ear containing, ARF binding protein 2) This gene encodes a member of the Golgi-localized, gamma adaptin ear-containing, ARF-binding (GGA) family. This family includes ubiquitous coat proteins that regulate the trafficking of proteins between the trans-Golgi network and the lysosome. These proteins share an amino-terminal VHS domain which mediates sorting of the mannose 6-phosphate receptors at the trans-Golgi network. They also contain a carboxy-terminal region with homology to the ear domain of gamma-adaptins. This family member may play a significant role in cargo molecules regulation and clathrin-coated vesicle assembly. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GGA2NM_015044.4 linkuse as main transcriptc.91+4968G>A intron_variant ENST00000309859.8
GGA2XM_047433801.1 linkuse as main transcriptc.62-9575G>A intron_variant
GGA2XM_047433802.1 linkuse as main transcriptc.-21+3945G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GGA2ENST00000309859.8 linkuse as main transcriptc.91+4968G>A intron_variant 1 NM_015044.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0462
AC:
7022
AN:
152000
Hom.:
578
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.159
Gnomad AMI
AF:
0.0186
Gnomad AMR
AF:
0.0197
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.000750
Gnomad OTH
AF:
0.0306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0462
AC:
7035
AN:
152118
Hom.:
579
Cov.:
32
AF XY:
0.0448
AC XY:
3334
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.159
Gnomad4 AMR
AF:
0.0196
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000721
Gnomad4 OTH
AF:
0.0302
Alfa
AF:
0.0549
Hom.:
85
Bravo
AF:
0.0523
Asia WGS
AF:
0.00779
AC:
27
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.76
DANN
Benign
0.77

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: rs739498; hg19: chr16-23516674; API