chr15-20534365-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001145004.2(GOLGA6L6):ā€‹c.2069A>Gā€‹(p.Glu690Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00010 ( 0 hom., cov: 17)
Exomes š‘“: 0.00014 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 missense

Scores

1
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.71
Variant links:
Genes affected
GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.067480326).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLGA6L6NM_001145004.2 linkc.2069A>G p.Glu690Gly missense_variant Exon 8 of 9 ENST00000619213.1 NP_001138476.2 A8MZA4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLGA6L6ENST00000619213.1 linkc.2069A>G p.Glu690Gly missense_variant Exon 8 of 9 5 NM_001145004.2 ENSP00000480376.1 A8MZA4

Frequencies

GnomAD3 genomes
AF:
0.000101
AC:
13
AN:
128882
Hom.:
0
Cov.:
17
show subpopulations
Gnomad AFR
AF:
0.0000322
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000197
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000108
AC:
14
AN:
129836
Hom.:
1
AF XY:
0.0000999
AC XY:
7
AN XY:
70058
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000277
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000140
AC:
177
AN:
1265236
Hom.:
0
Cov.:
29
AF XY:
0.000159
AC XY:
100
AN XY:
627098
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000631
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000171
Gnomad4 OTH exome
AF:
0.000131
GnomAD4 genome
AF:
0.000101
AC:
13
AN:
128882
Hom.:
0
Cov.:
17
AF XY:
0.000112
AC XY:
7
AN XY:
62700
show subpopulations
Gnomad4 AFR
AF:
0.0000322
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000197
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000192
Hom.:
0
ExAC
AF:
0.0000553
AC:
1

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Dec 26, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.2147A>G (p.E716G) alteration is located in exon 8 (coding exon 8) of the GOLGA6L6 gene. This alteration results from a A to G substitution at nucleotide position 2147, causing the glutamic acid (E) at amino acid position 716 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
14
DANN
Benign
0.36
DEOGEN2
Benign
0.030
T
Eigen
Benign
-0.78
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.026
N
LIST_S2
Benign
0.61
T
M_CAP
Benign
0.0042
T
MetaRNN
Benign
0.067
T
MetaSVM
Benign
-0.99
T
PrimateAI
Uncertain
0.58
T
Sift4G
Benign
0.085
T
Vest4
0.15
MVP
0.055
ClinPred
0.10
T
Varity_R
0.035
gMVP
0.0077

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: rs753562860; hg19: chr15-20739603; API