2-210318773-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 0.355 in 151,680 control chromosomes in the GnomAD database, including 9,741 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 0.36 ( 9741 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.465
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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 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:
0.355
AC:
53835
AN:
151562
Hom.:
9726
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.364
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.452
Gnomad ASJ
AF:
0.407
Gnomad EAS
AF:
0.454
Gnomad SAS
AF:
0.346
Gnomad FIN
AF:
0.367
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.355
AC:
53907
AN:
151680
Hom.:
9741
Cov.:
31
AF XY:
0.362
AC XY:
26804
AN XY:
74112
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.453
Gnomad4 ASJ
AF:
0.407
Gnomad4 EAS
AF:
0.453
Gnomad4 SAS
AF:
0.347
Gnomad4 FIN
AF:
0.367
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.378
Alfa
AF:
0.346
Hom.:
1843
Bravo
AF:
0.362
Asia WGS
AF:
0.447
AC:
1552
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.43
DANN
Benign
0.49

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: rs925274; hg19: chr2-211183497; API