GeneBe

rs1345182096

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004287.5(GOSR2):​c.95-6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000795 in 1,257,334 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 8.0e-7 ( 0 hom. )

Consequence

GOSR2
NM_004287.5 splice_region, intron

Scores

2
Splicing: ADA: 0.00005778
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.200

Publications

0 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOSR2NM_004287.5 linkc.95-6G>A splice_region_variant, intron_variant Intron 2 of 5 ENST00000640051.2 NP_004278.2 O14653-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOSR2ENST00000640051.2 linkc.95-6G>A splice_region_variant, intron_variant Intron 2 of 5 1 NM_004287.5 ENSP00000492751.1 O14653-1
ENSG00000262633ENST00000571841.1 linkn.95-6G>A splice_region_variant, intron_variant Intron 2 of 9 5 ENSP00000461460.1 E7EQ34

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000401
AC:
1
AN:
249136
AF XY:
0.00000741
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000889
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
7.95e-7
AC:
1
AN:
1257334
Hom.:
0
Cov.:
19
AF XY:
0.00000157
AC XY:
1
AN XY:
636034
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
29250
American (AMR)
AF:
0.00
AC:
0
AN:
44228
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24920
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38600
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81836
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53298
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4648
European-Non Finnish (NFE)
AF:
0.00000108
AC:
1
AN:
927186
Other (OTH)
AF:
0.00
AC:
0
AN:
53368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000248
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
CADD
Benign
9.5
DANN
Benign
0.73
PhyloP100
0.20
PromoterAI
-0.0062
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000058
dbscSNV1_RF
Benign
0.0040
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

Other links and lift over

dbSNP: rs1345182096; hg19: chr17-45008459; API