rs10868366

Variant names:

• chr9-86085145-G-T
• rs10868366
• NM_016548.4:c.-21-5804C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016548.4(GOLM1):​c.-21-5804C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,064 control chromosomes in the GnomAD database, including 7,543 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.24 (7543 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GOLM1 NM_016548.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 18 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

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.-21-5804C>A		intron	N/A	NP_057632.2
	GOLM1	NM_177937.3		c.-21-5804C>A		intron	N/A	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.-21-5804C>A		intron	N/A	ENSP00000373364.3	Q8NBJ4-1
	GOLM1	ENST00000388711.7	TSL:1	c.-21-5804C>A		intron	N/A	ENSP00000373363.3	Q8NBJ4-1
	GOLM1	ENST00000944326.1		c.-21-5804C>A		intron	N/A	ENSP00000614385.1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36657 AN: 151946 Hom.: 7521 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.212

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.242 AC: 36728 AN: 152064 Hom.: 7543 Cov.: 32 AF XY: 0.241 AC XY: 17909 AN XY: 74354

African (AFR) AF: 0.536 AC: 22196 AN: 41436

American (AMR) AF: 0.189 AC: 2882 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3466

East Asian (EAS) AF: 0.523 AC: 2703 AN: 5172

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4822

European-Finnish (FIN) AF: 0.0472 AC: 500 AN: 10602

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6446 AN: 67980

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.145 Hom.: 10115

Bravo AF: 0.267

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10868366; hg19: chr9-88700060;