ENST00000422488.1:n.1365+18781G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000422488.1(SLC26A5-AS1):​n.1365+18781G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,040 control chromosomes in the GnomAD database, including 1,234 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 0.12 ( 1234 hom., cov: 32)

Consequence

SLC26A5-AS1
ENST00000422488.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Publications

1 publications found
Variant links:
Genes affected
SLC26A5-AS1 (HGNC:55680): (SLC26A5 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC26A5-AS1NR_110141.1 linkn.1365+18781G>C intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC26A5-AS1ENST00000422488.1 linkn.1365+18781G>C intron_variant Intron 2 of 3 1
SLC26A5-AS1ENST00000660729.1 linkn.307+18781G>C intron_variant Intron 2 of 2
SLC26A5-AS1ENST00000841470.1 linkn.292+18781G>C intron_variant Intron 2 of 2
SLC26A5-AS1ENST00000841471.1 linkn.304+18781G>C intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.122
AC:
18546
AN:
151922
Hom.:
1224
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0833
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.0955
Gnomad EAS
AF:
0.0821
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.173
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.141
Gnomad OTH
AF:
0.114
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.122
AC:
18589
AN:
152040
Hom.:
1234
Cov.:
32
AF XY:
0.124
AC XY:
9225
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.0839
AC:
3480
AN:
41478
American (AMR)
AF:
0.128
AC:
1953
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.0955
AC:
331
AN:
3466
East Asian (EAS)
AF:
0.0823
AC:
426
AN:
5174
South Asian (SAS)
AF:
0.122
AC:
587
AN:
4818
European-Finnish (FIN)
AF:
0.173
AC:
1832
AN:
10568
Middle Eastern (MID)
AF:
0.0476
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
0.141
AC:
9591
AN:
67952
Other (OTH)
AF:
0.119
AC:
250
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
831
1661
2492
3322
4153
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
206
412
618
824
1030
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.129
Hom.:
169
Bravo
AF:
0.116
Asia WGS
AF:
0.137
AC:
479
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.2
DANN
Benign
0.73
PhyloP100
-0.025

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs17281921; hg19: chr7-103105896; API