rs16941382

Variant names:

• chr17-46966142-T-C
• rs16941382
• ENST00000571841.1:n.584-392T>C

Variant summary

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

The ENST00000571841.1(ENSG00000262633):​n.584-392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,210 control chromosomes in the GnomAD database, including 2,184 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 0.15 (2184 hom., cov: 32)
• Consequence: ENSG00000262633 ENST00000571841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 16 publications found

Genes affected

ENSG00000262633 (HGNC:):

GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000571841.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOSR2	NM_001321133.2		c.584-392T>C		intron	N/A	NP_001308062.1
	GOSR2	NR_148349.2		n.1822-392T>C		intron	N/A
	GOSR2	NR_148350.2		n.1681-392T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262633	ENST00000571841.1	TSL:5	n.584-392T>C		intron	N/A	ENSP00000461460.1
	GOSR2	ENST00000573224.2	TSL:5	c.584-392T>C		intron	N/A	ENSP00000461784.2
	GOSR2	ENST00000640723.1	TSL:5	c.521-392T>C		intron	N/A	ENSP00000492206.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23263 AN: 152092 Hom.: 2190 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.153 AC: 23250 AN: 152210 Hom.: 2184 Cov.: 32 AF XY: 0.156 AC XY: 11585 AN XY: 74410

African (AFR) AF: 0.0556 AC: 2309 AN: 41546

American (AMR) AF: 0.166 AC: 2529 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1332 AN: 5182

South Asian (SAS) AF: 0.145 AC: 701 AN: 4828

European-Finnish (FIN) AF: 0.250 AC: 2648 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12838 AN: 68004

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.172 Hom.: 3039

Bravo AF: 0.146

Asia WGS AF: 0.166 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		0.36
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: rs16941382; hg19: chr17-45043508;