Genetic Variant NM_018652.5:c.636C>T (chr15-72661335-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_018652.5(GOLGA6B):c.636C>T(p.Asn212Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00329 in 151,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 0 hom., cov: 23)

Exomes 𝑓: 0.0039 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6B
NM_018652.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.806

Variant links:

Genes affected

GOLGA6B (HGNC:32205): (golgin A6 family member B) This gene is found in a large, low copy repeat sequence or duplicon that is found in multiple copies, which are greater than 90% similar, on chromosome 15. Duplicons are associated with deletions, inversions and other chromosomal rearrangements that underlie genomic disease. This gene is a member of the golgin gene family, whose protein products localize to the Golgi apparatus. The majority of the related gene copies are thought to be transcribed pseudogenes. It is not known whether this gene is a pseudogene or if it encodes a golgin protein. [provided by RefSeq, Jul 2008]

GOLGA6B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 15-72661335-C-T is Benign according to our data. Variant chr15-72661335-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388120.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.806 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6B	NM_018652.5 link	c.636C>T	p.Asn212Asn	synonymous_variant	Exon 8 of 18	ENST00000421285.4	NP_061122.4	A6NDN3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6B	ENST00000421285.4 link	c.636C>T	p.Asn212Asn	synonymous_variant	Exon 8 of 18	1	NM_018652.5	ENSP00000408132.3		A6NDN3

Frequencies

GnomAD3 genomes

AF:

0.00329

AC:

498

AN:

151212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000922

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000768

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00831

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00510

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00299

AC:

730

AN:

244196

Hom.:

AF XY:

0.00291

AC XY:

387

AN XY:

132968

show subpopulations

Gnomad AFR exome

AF:

0.000745

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.000504

Gnomad EAS exome

AF:

0.000219

Gnomad SAS exome

AF:

0.000229

Gnomad FIN exome

AF:

0.00715

Gnomad NFE exome

AF:

0.00456

Gnomad OTH exome

AF:

0.00251

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00387

AC:

5602

AN:

1448652

Hom.:

Cov.:

AF XY:

0.00381

AC XY:

2747

AN XY:

721022

show subpopulations

Gnomad4 AFR exome

AF:

0.000869

Gnomad4 AMR exome

AF:

0.000987

Gnomad4 ASJ exome

AF:

0.000574

Gnomad4 EAS exome

AF:

0.000429

Gnomad4 SAS exome

AF:

0.000244

Gnomad4 FIN exome

AF:

0.00786

Gnomad4 NFE exome

AF:

0.00440

Gnomad4 OTH exome

AF:

0.00359

GnomAD4 genome

AF:

0.00329

AC:

498

AN:

151328

Hom.:

Cov.:

AF XY:

0.00316

AC XY:

234

AN XY:

74020

show subpopulations

Gnomad4 AFR

AF:

0.000919

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000770

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00831

Gnomad4 NFE

AF:

0.00510

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00580

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GOLGA6B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.9

DANN

Benign

0.67

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