2-20971074-G-A

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 0.256 in 152,184 control chromosomes in the GnomAD database, including 5,842 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 0.26 ( 5842 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0850
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.256
AC:
38897
AN:
152066
Hom.:
5845
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.239
Gnomad AMR
AF:
0.234
Gnomad ASJ
AF:
0.274
Gnomad EAS
AF:
0.718
Gnomad SAS
AF:
0.526
Gnomad FIN
AF:
0.274
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.236
Gnomad OTH
AF:
0.248
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.256
AC:
38903
AN:
152184
Hom.:
5842
Cov.:
33
AF XY:
0.262
AC XY:
19502
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.234
Gnomad4 ASJ
AF:
0.274
Gnomad4 EAS
AF:
0.718
Gnomad4 SAS
AF:
0.524
Gnomad4 FIN
AF:
0.274
Gnomad4 NFE
AF:
0.236
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.247
Hom.:
6319
Bravo
AF:
0.250
Asia WGS
AF:
0.586
AC:
2035
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.4
DANN
Benign
0.68

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: rs6728178; hg19: chr2-21193946; API