21-26868255-C-T

Variant summary

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

The XR_937632.3(LOC105372760):​n.323+13039C>T variant causes a intron, non coding transcript 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, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282
Variant links:
Genes affected

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=-0.8).
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/exons MANE UniProt
LOC105372760XR_937632.3 linkuse as main transcriptn.323+13039C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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
Gnomad4 AFR
AF:
0.305
Gnomad4 AMR
AF:
0.349
Gnomad4 ASJ
AF:
0.323
Gnomad4 EAS
AF:
0.0526
Gnomad4 SAS
AF:
0.348
Gnomad4 FIN
AF:
0.191
Gnomad4 NFE
AF:
0.360
Gnomad4 OTH
AF:
0.290
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

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: rs229109; hg19: chr21-28240574; API