Variant 15-20534450-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001145004.2(GOLGA6L6):c.1984G>A(p.Glu662Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000422 in 135,190 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).

Frequency

Genomes: 𝑓 0.00042 ( 0 hom., cov: 24)

Exomes 𝑓: 0.00020 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.30

Variant links:

Genes affected

GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

GOLGA6L6 links:

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=0.06514943).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA6L6	NM_001145004.2 linkuse as main transcript	c.1984G>A	p.Glu662Lys	missense_variant	8/9	ENST00000619213.1	NP_001138476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLGA6L6	ENST00000619213.1 linkuse as main transcript	c.1984G>A	p.Glu662Lys	missense_variant	8/9	5	NM_001145004.2	ENSP00000480376	P1

Frequencies

GnomAD3 genomes

AF:

0.000422

AC:

AN:

135084

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000861

Gnomad AMI

AF:

0.00134

Gnomad AMR

AF:

0.000367

Gnomad ASJ

AF:

0.000311

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00122

Gnomad FIN

AF:

0.000317

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000596

Gnomad OTH

AF:

0.00108

GnomAD3 exomes

AF:

0.00000703

AC:

AN:

142178

Hom.:

AF XY:

0.00

AC XY:

AN XY:

76126

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:

0.0000182

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000200

AC:

260

AN:

1298832

Hom.:

Cov.:

AF XY:

0.000189

AC XY:

121

AN XY:

641116

show subpopulations

Gnomad4 AFR exome

AF:

0.000109

Gnomad4 AMR exome

AF:

0.000587

Gnomad4 ASJ exome

AF:

0.000607

Gnomad4 EAS exome

AF:

0.0000652

Gnomad4 SAS exome

AF:

0.000362

Gnomad4 FIN exome

AF:

0.000617

Gnomad4 NFE exome

AF:

0.000147

Gnomad4 OTH exome

AF:

0.000413

GnomAD4 genome

AF:

0.000422

AC:

AN:

135190

Hom.:

Cov.:

AF XY:

0.000378

AC XY:

AN XY:

66064

show subpopulations

Gnomad4 AFR

AF:

0.0000858

Gnomad4 AMR

AF:

0.000367

Gnomad4 ASJ

AF:

0.000311

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00122

Gnomad4 FIN

AF:

0.000317

Gnomad4 NFE

AF:

0.000596

Gnomad4 OTH

AF:

0.00106

Alfa

AF:

0.000337

Hom.:

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 submitter

clinical testing

Ambry Genetics

Mar 18, 2024

The c.2062G>A (p.E688K) alteration is located in exon 8 (coding exon 8) of the GOLGA6L6 gene. This alteration results from a G to A substitution at nucleotide position 2062, causing the glutamic acid (E) at amino acid position 688 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

0.13

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.48

DEOGEN2

Benign

0.0059

Eigen

Benign

-0.90

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0085

LIST_S2

Benign

0.57

M_CAP

Benign

0.0024

MetaRNN

Benign

0.065

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.61

Sift4G

Benign

0.28

Vest4

0.12

MVP

0.030

ClinPred

0.20

Varity_R

0.032

gMVP

0.013

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over