Variant 9-86035405-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_016548.4(GOLM1):c.978C>T(p.Pro326=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00204 in 1,613,898 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 5 hom., cov: 30)

Exomes 𝑓: 0.0016 ( 19 hom. )

Consequence

GOLM1
NM_016548.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.94

Variant links:

Genes affected

GOLM1 (HGNC:15451): (golgi membrane protein 1) The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is a type II Golgi transmembrane protein. It processes proteins synthesized in the rough endoplasmic reticulum and assists in the transport of protein cargo through the Golgi apparatus. The expression of this gene has been observed to be upregulated in response to viral infection. Alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Sep 2009]

GOLM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 9-86035405-G-A is Benign according to our data. Variant chr9-86035405-G-A is described in ClinVar as [Benign]. Clinvar id is 713718.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.94 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00656 (997/152080) while in subpopulation AFR AF= 0.0191 (792/41494). AF 95% confidence interval is 0.018. There are 5 homozygotes in gnomad4. There are 478 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLM1	NM_016548.4 linkuse as main transcript	c.978C>T	p.Pro326=	synonymous_variant	8/10	ENST00000388712.7
GOLM1	NM_177937.3 linkuse as main transcript	c.978C>T	p.Pro326=	synonymous_variant	8/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLM1	ENST00000388712.7 linkuse as main transcript	c.978C>T	p.Pro326=	synonymous_variant	8/10	1	NM_016548.4	P1	Q8NBJ4-1
GOLM1	ENST00000388711.7 linkuse as main transcript	c.978C>T	p.Pro326=	synonymous_variant	8/10	1		P1	Q8NBJ4-1
GOLM1	ENST00000464314.1 linkuse as main transcript	n.687C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.00653

AC:

992

AN:

151962

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0190

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00361

Gnomad ASJ

AF:

0.0174

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.0000945

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00100

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00287

AC:

722

AN:

251328

Hom.:

AF XY:

0.00243

AC XY:

330

AN XY:

135838

show subpopulations

Gnomad AFR exome

AF:

0.0207

Gnomad AMR exome

AF:

0.00214

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00107

Gnomad OTH exome

AF:

0.00391

GnomAD4 exome

AF:

0.00157

AC:

2294

AN:

1461818

Hom.:

Cov.:

AF XY:

0.00151

AC XY:

1096

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.0234

Gnomad4 AMR exome

AF:

0.00239

Gnomad4 ASJ exome

AF:

0.0150

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000313

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.000620

Gnomad4 OTH exome

AF:

0.00437

GnomAD4 genome

AF:

0.00656

AC:

997

AN:

152080

Hom.:

Cov.:

AF XY:

0.00643

AC XY:

478

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0191

Gnomad4 AMR

AF:

0.00360

Gnomad4 ASJ

AF:

0.0174

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.0000945

Gnomad4 NFE

AF:

0.00100

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.00464

Hom.:

Bravo

AF:

0.00761

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00136

EpiControl

AF:

0.00172

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.13

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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