2-226275057-C-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 0.247 in 151,858 control chromosomes in the GnomAD database, including 5,841 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 0.25 ( 5841 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.67
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 (AFR) allele frequency at 95% confidence interval = 0.434 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:
0.246
AC:
37401
AN:
151740
Hom.:
5824
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.439
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.220
Gnomad ASJ
AF:
0.186
Gnomad EAS
AF:
0.336
Gnomad SAS
AF:
0.277
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.150
Gnomad OTH
AF:
0.207
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.247
AC:
37469
AN:
151858
Hom.:
5841
Cov.:
32
AF XY:
0.247
AC XY:
18338
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.439
Gnomad4 AMR
AF:
0.220
Gnomad4 ASJ
AF:
0.186
Gnomad4 EAS
AF:
0.336
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.139
Gnomad4 NFE
AF:
0.150
Gnomad4 OTH
AF:
0.215
Alfa
AF:
0.0993
Hom.:
156
Bravo
AF:
0.259
Asia WGS
AF:
0.410
AC:
1423
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.090
DANN
Benign
0.45

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: rs10167219; hg19: chr2-227139773; API