rs2216924

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 0.279 in 152,018 control chromosomes in the GnomAD database, including 5,989 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 0.28 ( 5989 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.110
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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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:
0.279
AC:
42415
AN:
151898
Hom.:
5985
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.246
Gnomad AMI
AF:
0.368
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.376
Gnomad EAS
AF:
0.171
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.317
Gnomad MID
AF:
0.350
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.279
AC:
42457
AN:
152018
Hom.:
5989
Cov.:
33
AF XY:
0.279
AC XY:
20708
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.253
Gnomad4 ASJ
AF:
0.376
Gnomad4 EAS
AF:
0.170
Gnomad4 SAS
AF:
0.312
Gnomad4 FIN
AF:
0.317
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.274
Alfa
AF:
0.284
Hom.:
1104
Bravo
AF:
0.273
Asia WGS
AF:
0.298
AC:
1034
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.6
DANN
Benign
0.28

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: rs2216924; hg19: chr2-67079943; API