chr2-121820466-A-G

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 0.745 in 152,172 control chromosomes in the GnomAD database, including 43,499 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 0.75 ( 43499 hom., cov: 34)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 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:
0.745
AC:
113288
AN:
152054
Hom.:
43456
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.780
Gnomad AMI
AF:
0.785
Gnomad AMR
AF:
0.633
Gnomad ASJ
AF:
0.838
Gnomad EAS
AF:
0.196
Gnomad SAS
AF:
0.724
Gnomad FIN
AF:
0.655
Gnomad MID
AF:
0.829
Gnomad NFE
AF:
0.800
Gnomad OTH
AF:
0.767
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.745
AC:
113386
AN:
152172
Hom.:
43499
Cov.:
34
AF XY:
0.733
AC XY:
54529
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.780
Gnomad4 AMR
AF:
0.632
Gnomad4 ASJ
AF:
0.838
Gnomad4 EAS
AF:
0.196
Gnomad4 SAS
AF:
0.726
Gnomad4 FIN
AF:
0.655
Gnomad4 NFE
AF:
0.800
Gnomad4 OTH
AF:
0.766
Alfa
AF:
0.790
Hom.:
25279
Bravo
AF:
0.739
Asia WGS
AF:
0.515
AC:
1795
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.36
DANN
Benign
0.29

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: rs7577075; hg19: chr2-122578042; API