GeneBe

chr21-26868255-C-T

Variant names:

Variant summary

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

The XR_937632.3(LOC105372760):​n.323+13039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,992 control chromosomes in the GnomAD database, including 8,150 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 0.32 ( 8150 hom., cov: 31)

Consequence

LOC105372760
XR_937632.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282

Publications

2 publications found
Variant links:
Genes affected

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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105372760XR_937632.3 linkn.323+13039C>T intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.319
AC:
48452
AN:
151872
Hom.:
8143
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.305
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.323
Gnomad EAS
AF:
0.0529
Gnomad SAS
AF:
0.348
Gnomad FIN
AF:
0.191
Gnomad MID
AF:
0.298
Gnomad NFE
AF:
0.360
Gnomad OTH
AF:
0.293
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.319
AC:
48486
AN:
151992
Hom.:
8150
Cov.:
31
AF XY:
0.310
AC XY:
23041
AN XY:
74318
show subpopulations
African (AFR)
AF:
0.305
AC:
12652
AN:
41446
American (AMR)
AF:
0.349
AC:
5327
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.323
AC:
1119
AN:
3466
East Asian (EAS)
AF:
0.0526
AC:
272
AN:
5168
South Asian (SAS)
AF:
0.348
AC:
1671
AN:
4802
European-Finnish (FIN)
AF:
0.191
AC:
2023
AN:
10572
Middle Eastern (MID)
AF:
0.307
AC:
89
AN:
290
European-Non Finnish (NFE)
AF:
0.360
AC:
24478
AN:
67958
Other (OTH)
AF:
0.290
AC:
610
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1669
3339
5008
6678
8347
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
486
972
1458
1944
2430
<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:
0.332
Hom.:
1065
Bravo
AF:
0.324
Asia WGS
AF:
0.205
AC:
717
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
4.8
DANN
Benign
0.57
PhyloP100
0.28

Splicing

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

Publications

Other links and lift over

dbSNP: rs229109; hg19: chr21-28240574; API