rs2351254

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 0.298 in 151,808 control chromosomes in the GnomAD database, including 11,755 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 0.30 ( 11755 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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:
0.298
AC:
45182
AN:
151690
Hom.:
11699
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.680
Gnomad AMI
AF:
0.0703
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.0988
Gnomad EAS
AF:
0.441
Gnomad SAS
AF:
0.0923
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.0858
Gnomad OTH
AF:
0.265
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45305
AN:
151808
Hom.:
11755
Cov.:
32
AF XY:
0.301
AC XY:
22364
AN XY:
74178
show subpopulations
Gnomad4 AFR
AF:
0.680
Gnomad4 AMR
AF:
0.356
Gnomad4 ASJ
AF:
0.0988
Gnomad4 EAS
AF:
0.441
Gnomad4 SAS
AF:
0.0934
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.0858
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.190
Hom.:
739
Bravo
AF:
0.334
Asia WGS
AF:
0.302
AC:
1051
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.57
DANN
Benign
0.18

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: rs2351254; hg19: chr15-89580299; API