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rs2282538

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The NR_135084.1(STX5-DT):n.27C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 596,750 control chromosomes in the GnomAD database, including 1,775 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 0.071 ( 417 hom., cov: 31)
Exomes 𝑓: 0.068 ( 1358 hom. )

Consequence

STX5-DT
NR_135084.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.57
Variant links:
Genes affected
STX5-DT (HGNC:55488): (STX5 divergent transcript)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.15).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STX5-DTNR_135084.1 linkuse as main transcriptn.27C>T non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STX5-DTENST00000535817.1 linkuse as main transcriptn.27C>T non_coding_transcript_exon_variant 1/23

Frequencies

GnomAD3 genomes
AF:
0.0708
AC:
10763
AN:
152042
Hom.:
418
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0914
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.0432
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.0754
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0531
Gnomad OTH
AF:
0.0651
GnomAD4 exome
AF:
0.0679
AC:
30200
AN:
444590
Hom.:
1358
Cov.:
0
AF XY:
0.0702
AC XY:
16411
AN XY:
233748
show subpopulations
Gnomad4 AFR exome
AF:
0.0910
Gnomad4 AMR exome
AF:
0.0343
Gnomad4 ASJ exome
AF:
0.139
Gnomad4 EAS exome
AF:
0.154
Gnomad4 SAS exome
AF:
0.0937
Gnomad4 FIN exome
AF:
0.0686
Gnomad4 NFE exome
AF:
0.0512
Gnomad4 OTH exome
AF:
0.0655
GnomAD4 genome
AF:
0.0709
AC:
10786
AN:
152160
Hom.:
417
Cov.:
31
AF XY:
0.0730
AC XY:
5432
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0915
Gnomad4 AMR
AF:
0.0432
Gnomad4 ASJ
AF:
0.135
Gnomad4 EAS
AF:
0.146
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.0754
Gnomad4 NFE
AF:
0.0531
Gnomad4 OTH
AF:
0.0696
Alfa
AF:
0.0645
Hom.:
60
Bravo
AF:
0.0682
Asia WGS
AF:
0.114
AC:
394
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.15
Cadd
Benign
18
Dann
Benign
0.94

Splicing

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: rs2282538; hg19: chr11-62599732; API