rs143510742

Variant names:

• chr9-86035513-G-A
• rs143510742
• NM_016548.4:c.870C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-86035513-G-A
• chr9-86035513-G-C
• chr9-86035513-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_016548.4(GOLM1):​c.870C>T​(p.Phe290Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000283 in 1,612,644 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 Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0012 (0 hom., cov: 29)
  • Exomes 𝑓: 0.00019 (0 hom.)
• Consequence: GOLM1 NM_016548.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.80
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 9-86035513-G-A is Benign according to our data. Variant chr9-86035513-G-A is described in ClinVar as Benign. ClinVar VariationId is 716391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.8 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016548.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLM1	NM_016548.4	MANE Select	c.870C>T	p.Phe290Phe	synonymous	Exon 8 of 10	NP_057632.2
	GOLM1	NM_177937.3		c.870C>T	p.Phe290Phe	synonymous	Exon 8 of 10	NP_808800.1	Q8NBJ4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLM1	ENST00000388712.7	TSL:1 MANE Select	c.870C>T	p.Phe290Phe	synonymous	Exon 8 of 10	ENSP00000373364.3	Q8NBJ4-1
	GOLM1	ENST00000388711.7	TSL:1	c.870C>T	p.Phe290Phe	synonymous	Exon 8 of 10	ENSP00000373363.3	Q8NBJ4-1
	GOLM1	ENST00000944326.1		c.912C>T	p.Phe304Phe	synonymous	Exon 8 of 10	ENSP00000614385.1

Frequencies

GnomAD3 genomes AF: 0.00115 AC: 175 AN: 151826 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00390

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000883

Gnomad OTH AF: 0.000960

GnomAD2 exomes AF: 0.000431 AC: 108 AN: 250590 AF XY: 0.000369

Gnomad AFR exome AF: 0.00443

Gnomad AMR exome AF: 0.000434

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000489

Gnomad FIN exome AF: 0.0000481

Gnomad NFE exome AF: 0.0000791

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000192 AC: 281 AN: 1460700 Hom.: 0 Cov.: 35 AF XY: 0.000169 AC XY: 123 AN XY: 726728

African (AFR) AF: 0.00415 AC: 139 AN: 33480

American (AMR) AF: 0.000559 AC: 25 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.000176 AC: 7 AN: 39700

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52250

Middle Eastern (MID) AF: 0.00191 AC: 11 AN: 5768

European-Non Finnish (NFE) AF: 0.0000594 AC: 66 AN: 1112002

Other (OTH) AF: 0.000530 AC: 32 AN: 60384

GnomAD4 genome AF: 0.00115 AC: 175 AN: 151944 Hom.: 0 Cov.: 29 AF XY: 0.00116 AC XY: 86 AN XY: 74276

African (AFR) AF: 0.00388 AC: 161 AN: 41446

American (AMR) AF: 0.000328 AC: 5 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5122

South Asian (SAS) AF: 0.00 AC: 0 AN: 4802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000883 AC: 6 AN: 67934

Other (OTH) AF: 0.000950 AC: 2 AN: 2106

Alfa AF: 0.000524 Hom.: 0

Bravo AF: 0.00135

EpiCase AF: 0.000109

EpiControl AF: 0.000178

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs143510742; hg19: chr9-88650428; COSMIC: COSV57416078; COSMIC: COSV57416078;