rs3785889

Positions:

• chr17-46928464-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004287.5(GOSR2):​c.30-1056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,842 control chromosomes in the GnomAD database, including 15,847 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 0.45 (15847 hom., cov: 30)
• Consequence: GOSR2 NM_004287.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOSR2	NM_004287.5	c.30-1056G>A		intron_variant		ENST00000640051.2	NP_004278.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOSR2	ENST00000640051.2	c.30-1056G>A		intron_variant		1	NM_004287.5	ENSP00000492751.1
ENSG00000262633	ENST00000571841.1	n.30-1056G>A		intron_variant		5		ENSP00000461460.1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68486 AN: 151724 Hom.: 15824 Cov.: 30

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.451 AC: 68551 AN: 151842 Hom.: 15847 Cov.: 30 AF XY: 0.450 AC XY: 33363 AN XY: 74218

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.443

Alfa AF: 0.485 Hom.: 4399

Bravo AF: 0.440

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.72

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: rs3785889; hg19: chr17-45005830;