20-24790872-T-C

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 0.508 in 152,144 control chromosomes in the GnomAD database, including 20,842 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 0.51 ( 20842 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.17
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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:
0.508
AC:
77232
AN:
152026
Hom.:
20838
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.352
Gnomad AMI
AF:
0.668
Gnomad AMR
AF:
0.528
Gnomad ASJ
AF:
0.476
Gnomad EAS
AF:
0.954
Gnomad SAS
AF:
0.586
Gnomad FIN
AF:
0.550
Gnomad MID
AF:
0.598
Gnomad NFE
AF:
0.550
Gnomad OTH
AF:
0.551
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.508
AC:
77262
AN:
152144
Hom.:
20842
Cov.:
33
AF XY:
0.512
AC XY:
38077
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.352
Gnomad4 AMR
AF:
0.527
Gnomad4 ASJ
AF:
0.476
Gnomad4 EAS
AF:
0.955
Gnomad4 SAS
AF:
0.585
Gnomad4 FIN
AF:
0.550
Gnomad4 NFE
AF:
0.550
Gnomad4 OTH
AF:
0.551
Alfa
AF:
0.504
Hom.:
2533
Bravo
AF:
0.502
Asia WGS
AF:
0.732
AC:
2545
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.20
DANN
Benign
0.28

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: rs226677; hg19: chr20-24771508; API