Genetic Variant GOLGA6L7:p.Arg140Trp (chr15-28845573-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001365371.2(GOLGA6L7):c.418C>T(p.Arg140Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00071 in 771,740 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00043 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00078 ( 7 hom. )

Consequence

GOLGA6L7
NM_001365371.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.76

Variant links:

Genes affected

GOLGA6L7 (HGNC:37442): (golgin A6 family like 7) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA6L7 links:

ENSG00000291258 (HGNC:):

ENSG00000291258 links:

PDCD6IPP2 (HGNC:49873): (PDCD6IP pseudogene 2)

PDCD6IPP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011129916).

BP6

Variant 15-28845573-G-A is Benign according to our data. Variant chr15-28845573-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3770845.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L7	NM_001365371.2 link	c.418C>T	p.Arg140Trp	missense_variant	Exon 6 of 9	ENST00000567390.7	NP_001352300.1
PDCD6IPP2	NR_037599.1 link	n.1561-1166G>A		intron_variant	Intron 12 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L7	ENST00000567390.7 link	c.418C>T	p.Arg140Trp	missense_variant	Exon 6 of 9	5	NM_001365371.2	ENSP00000490318.1		A0A1B0GV03

Frequencies

GnomAD3 genomes

AF:

0.000434

AC:

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000785

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00539

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.00102

AC:

148

AN:

144856

Hom.:

AF XY:

0.00139

AC XY:

108

AN XY:

77938

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000929

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000904

Gnomad SAS exome

AF:

0.00446

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000338

Gnomad OTH exome

AF:

0.000459

GnomAD4 exome

AF:

0.000778

AC:

482

AN:

619430

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

338

AN XY:

331202

show subpopulations

Gnomad4 AFR exome

AF:

0.000117

Gnomad4 AMR exome

AF:

0.000859

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000307

Gnomad4 SAS exome

AF:

0.00463

Gnomad4 FIN exome

AF:

0.0000293

Gnomad4 NFE exome

AF:

0.000284

Gnomad4 OTH exome

AF:

0.000425

GnomAD4 genome

AF:

0.000433

AC:

AN:

152310

Hom.:

Cov.:

AF XY:

0.000537

AC XY:

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0000962

Gnomad4 AMR

AF:

0.000784

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000309

Gnomad4 OTH

AF:

0.000948

Alfa

AF:

0.000342

Hom.:

Bravo

AF:

0.000298

ExAC

AF:

0.000657

AC:

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA6L7: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_noAF

Benign

-0.99

CADD

Benign

DANN

Benign

0.54

FATHMM_MKL

Benign

0.012

LIST_S2

Uncertain

0.91

MetaRNN

Benign

0.011

GERP RS

-0.62

Varity_R

0.17

gMVP

0.034

Splicing

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