rs2202063

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 151,992 control chromosomes in the GnomAD database, including 9,994 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 ( 9994 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.630
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 (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.355
AC:
53954
AN:
151876
Hom.:
9987
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.454
Gnomad AMI
AF:
0.418
Gnomad AMR
AF:
0.285
Gnomad ASJ
AF:
0.356
Gnomad EAS
AF:
0.275
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.330
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.355
AC:
53993
AN:
151992
Hom.:
9994
Cov.:
32
AF XY:
0.351
AC XY:
26080
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.454
Gnomad4 AMR
AF:
0.284
Gnomad4 ASJ
AF:
0.356
Gnomad4 EAS
AF:
0.276
Gnomad4 SAS
AF:
0.310
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.330
Gnomad4 OTH
AF:
0.346
Alfa
AF:
0.356
Hom.:
1250
Bravo
AF:
0.356
Asia WGS
AF:
0.317
AC:
1101
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
0.48
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: rs2202063; hg19: chr18-66966676; API