15-23129919-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001001413.3(GOLGA6L1):​c.1534C>T​(p.Arg512Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 119,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00049 ( 0 hom., cov: 25)
Exomes 𝑓: 0.00070 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GOLGA6L1
NM_001001413.3 missense

Scores

10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.18
Variant links:
Genes affected
GOLGA6L1 (HGNC:37444): (golgin A6 family like 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.069962084).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLGA6L1NM_001001413.3 linkc.1534C>T p.Arg512Trp missense_variant Exon 8 of 9 ENST00000614055.2 NP_001001413.3 Q8N7Z2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLGA6L1ENST00000614055.2 linkc.1534C>T p.Arg512Trp missense_variant Exon 8 of 9 5 NM_001001413.3 ENSP00000478478.1 Q8N7Z2

Frequencies

GnomAD3 genomes
AF:
0.000494
AC:
59
AN:
119330
Hom.:
0
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.000157
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:
0.000940
Gnomad OTH
AF:
0.000635
GnomAD3 exomes
AF:
0.0000734
AC:
10
AN:
136190
Hom.:
3
AF XY:
0.0000551
AC XY:
4
AN XY:
72644
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000285
Gnomad SAS exome
AF:
0.000148
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000773
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000697
AC:
430
AN:
617100
Hom.:
0
Cov.:
8
AF XY:
0.000644
AC XY:
210
AN XY:
326014
show subpopulations
Gnomad4 AFR exome
AF:
0.000112
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000675
Gnomad4 SAS exome
AF:
0.0000519
Gnomad4 FIN exome
AF:
0.0000746
Gnomad4 NFE exome
AF:
0.000983
Gnomad4 OTH exome
AF:
0.00120
GnomAD4 genome
AF:
0.000494
AC:
59
AN:
119416
Hom.:
0
Cov.:
25
AF XY:
0.000491
AC XY:
28
AN XY:
57012
show subpopulations
Gnomad4 AFR
AF:
0.000156
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:
0.000940
Gnomad4 OTH
AF:
0.000631
Alfa
AF:
0.000741
Hom.:
0
ExAC
AF:
0.0000494
AC:
1

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Sep 16, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1534C>T (p.R512W) alteration is located in exon 8 (coding exon 8) of the GOLGA6L1 gene. This alteration results from a C to T substitution at nucleotide position 1534, causing the arginine (R) at amino acid position 512 to be replaced by a tryptophan (W). 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
0.12
BayesDel_addAF
Benign
-0.36
T
BayesDel_noAF
Benign
-0.76
CADD
Benign
13
DANN
Benign
0.31
FATHMM_MKL
Benign
0.00049
N
LIST_S2
Benign
0.18
T
M_CAP
Benign
0.0047
T
MetaRNN
Benign
0.070
T
Sift4G
Benign
0.068
T
Vest4
0.12
MVP
0.14
GERP RS
-0.26
Varity_R
0.11
gMVP
0.025

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: rs370904969; hg19: chr15-23407359; API