21-33981573-G-T

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 0.379 in 151,926 control chromosomes in the GnomAD database, including 12,142 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 0.38 ( 12142 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.379
AC:
57535
AN:
151808
Hom.:
12117
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.574
Gnomad AMI
AF:
0.230
Gnomad AMR
AF:
0.402
Gnomad ASJ
AF:
0.333
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.206
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.379
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57599
AN:
151926
Hom.:
12142
Cov.:
31
AF XY:
0.372
AC XY:
27622
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.573
Gnomad4 AMR
AF:
0.402
Gnomad4 ASJ
AF:
0.333
Gnomad4 EAS
AF:
0.322
Gnomad4 SAS
AF:
0.326
Gnomad4 FIN
AF:
0.206
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.375
Alfa
AF:
0.237
Hom.:
745
Bravo
AF:
0.408
Asia WGS
AF:
0.295
AC:
1028
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.019
DANN
Benign
0.64

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: rs2070513; hg19: chr21-35353874; API