21-33395791-A-G

Variant summary

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

The variant allele was found at a frequency of 0.659 in 151,980 control chromosomes in the GnomAD database, including 34,565 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 0.66 ( 34565 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.658
AC:
99996
AN:
151862
Hom.:
34509
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.891
Gnomad AMI
AF:
0.488
Gnomad AMR
AF:
0.583
Gnomad ASJ
AF:
0.576
Gnomad EAS
AF:
0.594
Gnomad SAS
AF:
0.652
Gnomad FIN
AF:
0.546
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.647
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.659
AC:
100103
AN:
151980
Hom.:
34565
Cov.:
30
AF XY:
0.655
AC XY:
48681
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.891
Gnomad4 AMR
AF:
0.583
Gnomad4 ASJ
AF:
0.576
Gnomad4 EAS
AF:
0.594
Gnomad4 SAS
AF:
0.651
Gnomad4 FIN
AF:
0.546
Gnomad4 NFE
AF:
0.564
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.580
Hom.:
33748
Bravo
AF:
0.670
Asia WGS
AF:
0.671
AC:
2332
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.61
DANN
Benign
0.76

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: rs9976971; hg19: chr21-34768097; API