rs1867237

Variant names:

• chr17-46926463-G-A
• rs1867237
• NM_004287.5:c.30-3057G>A

Variant summary

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

The NM_004287.5(GOSR2):​c.30-3057G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,926 control chromosomes in the GnomAD database, including 26,878 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 0.59 (26878 hom., cov: 31)
• Consequence: GOSR2 NM_004287.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 10 publications found

Genes affected

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]

ENSG00000262633 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOSR2	NM_004287.5	c.30-3057G>A		intron_variant	Intron 1 of 5	ENST00000640051.2	NP_004278.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOSR2	ENST00000640051.2	c.30-3057G>A		intron_variant	Intron 1 of 5	1	NM_004287.5	ENSP00000492751.1
ENSG00000262633	ENST00000571841.1	n.30-3057G>A		intron_variant	Intron 1 of 9	5		ENSP00000461460.1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90277 AN: 151808 Hom.: 26849 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.595 AC: 90355 AN: 151926 Hom.: 26878 Cov.: 31 AF XY: 0.592 AC XY: 43963 AN XY: 74226

African (AFR) AF: 0.573 AC: 23721 AN: 41428

American (AMR) AF: 0.573 AC: 8753 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2866 AN: 5162

South Asian (SAS) AF: 0.519 AC: 2502 AN: 4820

European-Finnish (FIN) AF: 0.591 AC: 6228 AN: 10536

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41981 AN: 67936

Other (OTH) AF: 0.592 AC: 1246 AN: 2104

Alfa AF: 0.602 Hom.: 4867

Bravo AF: 0.595

Asia WGS AF: 0.547 AC: 1901 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	1.8
DANN	Benign	0.32
PhyloP100		-0.62
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: rs1867237; hg19: chr17-45003829;