chr17-46926463-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.621
Variant links:
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]
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
GOSR2NM_004287.5 linkuse as main transcriptc.30-3057G>A intron_variant ENST00000640051.2 NP_004278.2 O14653-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GOSR2ENST00000640051.2 linkuse as main transcriptc.30-3057G>A intron_variant 1 NM_004287.5 ENSP00000492751.1 O14653-1
ENSG00000262633ENST00000571841.1 linkuse as main transcriptn.30-3057G>A intron_variant 5 ENSP00000461460.1 E7EQ34

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90277
AN:
151808
Hom.:
26849
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.573
Gnomad4 AMR
AF:
0.573
Gnomad4 ASJ
AF:
0.693
Gnomad4 EAS
AF:
0.555
Gnomad4 SAS
AF:
0.519
Gnomad4 FIN
AF:
0.591
Gnomad4 NFE
AF:
0.618
Gnomad4 OTH
AF:
0.592
Alfa
AF:
0.603
Hom.:
4736
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1867237; hg19: chr17-45003829; API