rs2281517

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 0.209 in 152,174 control chromosomes in the GnomAD database, including 3,617 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 ( 3616 hom., cov: 32)
Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.415
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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:
0.209
AC:
31729
AN:
152050
Hom.:
3607
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.178
Gnomad AMI
AF:
0.305
Gnomad AMR
AF:
0.151
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.388
Gnomad SAS
AF:
0.362
Gnomad FIN
AF:
0.212
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.213
GnomAD4 exome
AF:
0.667
AC:
4
AN:
6
Hom.:
1
AF XY:
0.667
AC XY:
4
AN XY:
6
show subpopulations
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.209
AC:
31756
AN:
152168
Hom.:
3616
Cov.:
32
AF XY:
0.211
AC XY:
15699
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.178
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.388
Gnomad4 SAS
AF:
0.362
Gnomad4 FIN
AF:
0.212
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.222
Alfa
AF:
0.204
Hom.:
297
Bravo
AF:
0.197
Asia WGS
AF:
0.344
AC:
1196
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
8.5
DANN
Benign
0.63

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: rs2281517; hg19: chr14-94789787; API