9-86078545-C-T

Variant names:

• chr9-86078545-C-T
• rs7019241
• NM_016548.4:c.129+647G>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.129+647G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,836 control chromosomes in the GnomAD database, including 3,984 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 0.19 (3984 hom., cov: 32)
• Consequence: GOLM1 NM_016548.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 16 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLM1	NM_016548.4	c.129+647G>A		intron_variant	Intron 2 of 9	ENST00000388712.7	NP_057632.2
GOLM1	NM_177937.3	c.129+647G>A		intron_variant	Intron 2 of 9		NP_808800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLM1	ENST00000388712.7	c.129+647G>A		intron_variant	Intron 2 of 9	1	NM_016548.4	ENSP00000373364.3

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28324 AN: 151716 Hom.: 3980 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.187 AC: 28353 AN: 151836 Hom.: 3984 Cov.: 32 AF XY: 0.188 AC XY: 13972 AN XY: 74208

African (AFR) AF: 0.344 AC: 14199 AN: 41332

American (AMR) AF: 0.169 AC: 2582 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2739 AN: 5092

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4810

European-Finnish (FIN) AF: 0.0475 AC: 502 AN: 10566

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6403 AN: 67988

Other (OTH) AF: 0.180 AC: 379 AN: 2106

Alfa AF: 0.135 Hom.: 5523

Bravo AF: 0.205

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.57
PhyloP100		-1.5
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: rs7019241; hg19: chr9-88693460;