15-82344626-C-T

Variant summary

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

The NM_001164465.3(GOLGA6L10):​c.1234G>A​(p.Glu412Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 148,114 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000068 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00081 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GOLGA6L10
NM_001164465.3 missense

Scores

2
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.654
Variant links:
Genes affected
GOLGA6L10 (HGNC:37228): (golgin A6 family like 10)

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=0.09367889).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GOLGA6L10NM_001164465.3 linkc.1234G>A p.Glu412Lys missense_variant 6/9 ENST00000610657.2 NP_001157937.2 A6NI86

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GOLGA6L10ENST00000610657.2 linkc.1234G>A p.Glu412Lys missense_variant 6/92 NM_001164465.3 ENSP00000479362.1 A6NI86
GOLGA6L10ENST00000621197.4 linkc.985G>A p.Glu329Lys missense_variant 7/105 ENSP00000484254.2 A0A087X1J3

Frequencies

GnomAD3 genomes
AF:
0.0000675
AC:
10
AN:
148114
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000524
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:
0.000192
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000738
Gnomad OTH
AF:
0.000483
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000808
AC:
1131
AN:
1400124
Hom.:
0
Cov.:
36
AF XY:
0.000764
AC XY:
530
AN XY:
693450
show subpopulations
Gnomad4 AFR exome
AF:
0.0000960
Gnomad4 AMR exome
AF:
0.000221
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000526
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.000446
Gnomad4 NFE exome
AF:
0.000972
Gnomad4 OTH exome
AF:
0.000496
GnomAD4 genome
AF:
0.0000675
AC:
10
AN:
148114
Hom.:
0
Cov.:
31
AF XY:
0.0000830
AC XY:
6
AN XY:
72306
show subpopulations
Gnomad4 AFR
AF:
0.0000524
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000192
Gnomad4 NFE
AF:
0.0000738
Gnomad4 OTH
AF:
0.000483

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 14, 2024The c.1105G>A (p.E369K) alteration is located in exon 6 (coding exon 6) of the GOLGA6L10 gene. This alteration results from a G to A substitution at nucleotide position 1105, causing the glutamic acid (E) at amino acid position 369 to be replaced by a lysine (K). 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
0.20
BayesDel_addAF
Benign
-0.44
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
8.0
DANN
Uncertain
0.99
DEOGEN2
Benign
0.025
.;.;T
FATHMM_MKL
Benign
0.0034
N
LIST_S2
Benign
0.52
T;T;T
M_CAP
Benign
0.0022
T
MetaRNN
Benign
0.094
T;T;T
PrimateAI
Uncertain
0.78
T
Sift4G
Benign
0.65
T;T;T
Vest4
0.23
MVP
0.014
Varity_R
0.10
gMVP
0.069

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: rs1397222807; hg19: chr15-83013265; API