21-31793549-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 0.585 in 152,032 control chromosomes in the GnomAD database, including 26,784 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 0.59 ( 26784 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.33
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=-0.76).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 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:
0.585
AC:
88883
AN:
151914
Hom.:
26766
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.717
Gnomad AMI
AF:
0.477
Gnomad AMR
AF:
0.570
Gnomad ASJ
AF:
0.465
Gnomad EAS
AF:
0.773
Gnomad SAS
AF:
0.693
Gnomad FIN
AF:
0.584
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.495
Gnomad OTH
AF:
0.552
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.585
AC:
88946
AN:
152032
Hom.:
26784
Cov.:
33
AF XY:
0.591
AC XY:
43948
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.716
Gnomad4 AMR
AF:
0.570
Gnomad4 ASJ
AF:
0.465
Gnomad4 EAS
AF:
0.772
Gnomad4 SAS
AF:
0.693
Gnomad4 FIN
AF:
0.584
Gnomad4 NFE
AF:
0.495
Gnomad4 OTH
AF:
0.555
Alfa
AF:
0.429
Hom.:
1216
Bravo
AF:
0.587
Asia WGS
AF:
0.752
AC:
2613
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
18
DANN
Benign
0.65

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: rs1537096; hg19: chr21-33165862; API