2-211171950-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 0.734 in 151,820 control chromosomes in the GnomAD database, including 41,186 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 0.73 ( 41186 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40
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 = 0.807 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:
0.734
AC:
111319
AN:
151702
Hom.:
41162
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.800
Gnomad AMI
AF:
0.631
Gnomad AMR
AF:
0.722
Gnomad ASJ
AF:
0.652
Gnomad EAS
AF:
0.828
Gnomad SAS
AF:
0.664
Gnomad FIN
AF:
0.723
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.702
Gnomad OTH
AF:
0.721
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.734
AC:
111398
AN:
151820
Hom.:
41186
Cov.:
31
AF XY:
0.734
AC XY:
54415
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.799
Gnomad4 AMR
AF:
0.722
Gnomad4 ASJ
AF:
0.652
Gnomad4 EAS
AF:
0.828
Gnomad4 SAS
AF:
0.663
Gnomad4 FIN
AF:
0.723
Gnomad4 NFE
AF:
0.702
Gnomad4 OTH
AF:
0.724
Alfa
AF:
0.722
Hom.:
6729
Bravo
AF:
0.740
Asia WGS
AF:
0.749
AC:
2600
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.19
DANN
Benign
0.44

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: rs1437933; hg19: chr2-212036675; API