rs2320289

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 0.211 in 152,126 control chromosomes in the GnomAD database, including 3,629 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 0.21 ( 3629 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288
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=-0.57).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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:
0.211
AC:
32044
AN:
152008
Hom.:
3611
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.249
Gnomad AMR
AF:
0.280
Gnomad ASJ
AF:
0.157
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.174
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.223
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32081
AN:
152126
Hom.:
3629
Cov.:
33
AF XY:
0.214
AC XY:
15935
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.204
Gnomad4 AMR
AF:
0.281
Gnomad4 ASJ
AF:
0.157
Gnomad4 EAS
AF:
0.484
Gnomad4 SAS
AF:
0.172
Gnomad4 FIN
AF:
0.174
Gnomad4 NFE
AF:
0.189
Gnomad4 OTH
AF:
0.229
Alfa
AF:
0.193
Hom.:
2902
Bravo
AF:
0.222
Asia WGS
AF:
0.350
AC:
1216
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
2.8
DANN
Benign
0.52

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: rs2320289; hg19: chr4-18162104; API