2-20981153-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 0.242 in 152,094 control chromosomes in the GnomAD database, including 5,507 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 0.24 ( 5507 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379
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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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:
0.242
AC:
36757
AN:
151974
Hom.:
5508
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.149
Gnomad AMI
AF:
0.239
Gnomad AMR
AF:
0.230
Gnomad ASJ
AF:
0.275
Gnomad EAS
AF:
0.726
Gnomad SAS
AF:
0.535
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.318
Gnomad NFE
AF:
0.237
Gnomad OTH
AF:
0.241
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.242
AC:
36752
AN:
152094
Hom.:
5507
Cov.:
32
AF XY:
0.249
AC XY:
18525
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.149
Gnomad4 AMR
AF:
0.230
Gnomad4 ASJ
AF:
0.275
Gnomad4 EAS
AF:
0.726
Gnomad4 SAS
AF:
0.533
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.237
Gnomad4 OTH
AF:
0.246
Alfa
AF:
0.263
Hom.:
7866
Bravo
AF:
0.233
Asia WGS
AF:
0.586
AC:
2034
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.15
DANN
Benign
0.32

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: rs6544366; hg19: chr2-21204025; API