rs10868366

Positions:

• chr9-86085145-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLM1	NM_016548.4	c.-21-5804C>A		intron_variant		ENST00000388712.7	NP_057632.2
GOLM1	NM_177937.3	c.-21-5804C>A		intron_variant			NP_808800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLM1	ENST00000388712.7	c.-21-5804C>A		intron_variant		1	NM_016548.4	ENSP00000373364.3
GOLM1	ENST00000388711.7	c.-21-5804C>A		intron_variant		1		ENSP00000373363.3
GOLM1	ENST00000466178.1	c.-141-106C>A		intron_variant		4		ENSP00000418155.1
GOLM1	ENST00000472919.1	n.150-5804C>A		intron_variant		4

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

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.216

Alfa AF: 0.125 Hom.: 3108

Bravo AF: 0.267

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs10868366; hg19: chr9-88700060;