chr9-86046571-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_016548.4(GOLM1):​c.366C>T​(p.Asp122=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000743 in 1,596,644 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00040 ( 4 hom. )

Consequence

GOLM1
NM_016548.4 splice_region, synonymous

Scores

2
Splicing: ADA: 0.003179
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.698
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 9-86046571-G-A is Benign according to our data. Variant chr9-86046571-G-A is described in ClinVar as [Benign]. Clinvar id is 791300.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.698 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GOLM1NM_016548.4 linkuse as main transcriptc.366C>T p.Asp122= splice_region_variant, synonymous_variant 5/10 ENST00000388712.7
GOLM1NM_177937.3 linkuse as main transcriptc.366C>T p.Asp122= splice_region_variant, synonymous_variant 5/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GOLM1ENST00000388712.7 linkuse as main transcriptc.366C>T p.Asp122= splice_region_variant, synonymous_variant 5/101 NM_016548.4 P1Q8NBJ4-1

Frequencies

GnomAD3 genomes
AF:
0.00398
AC:
605
AN:
152110
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0138
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00431
GnomAD3 exomes
AF:
0.00112
AC:
273
AN:
242794
Hom.:
2
AF XY:
0.000717
AC XY:
94
AN XY:
131114
show subpopulations
Gnomad AFR exome
AF:
0.0155
Gnomad AMR exome
AF:
0.000861
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000339
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000334
GnomAD4 exome
AF:
0.000402
AC:
581
AN:
1444416
Hom.:
4
Cov.:
27
AF XY:
0.000334
AC XY:
240
AN XY:
719116
show subpopulations
Gnomad4 AFR exome
AF:
0.0149
Gnomad4 AMR exome
AF:
0.000862
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000273
Gnomad4 OTH exome
AF:
0.000769
GnomAD4 genome
AF:
0.00397
AC:
605
AN:
152228
Hom.:
5
Cov.:
32
AF XY:
0.00356
AC XY:
265
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0138
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00427
Alfa
AF:
0.000695
Hom.:
1
Bravo
AF:
0.00485
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

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 submitterclinical testingInvitaeJun 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
10
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0032
dbscSNV1_RF
Benign
0.078
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: rs12350451; hg19: chr9-88661486; API