rs2542151

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.831 in 152,208 control chromosomes in the GnomAD database, including 52,673 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 0.83 ( 52673 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.831
AC:
126378
AN:
152090
Hom.:
52623
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.792
Gnomad AMI
AF:
0.954
Gnomad AMR
AF:
0.858
Gnomad ASJ
AF:
0.906
Gnomad EAS
AF:
0.833
Gnomad SAS
AF:
0.813
Gnomad FIN
AF:
0.861
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.839
Gnomad OTH
AF:
0.844
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.831
AC:
126486
AN:
152208
Hom.:
52673
Cov.:
32
AF XY:
0.831
AC XY:
61863
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.792
AC:
0.792371
AN:
0.792371
Gnomad4 AMR
AF:
0.857
AC:
0.857348
AN:
0.857348
Gnomad4 ASJ
AF:
0.906
AC:
0.90634
AN:
0.90634
Gnomad4 EAS
AF:
0.832
AC:
0.832043
AN:
0.832043
Gnomad4 SAS
AF:
0.814
AC:
0.8139
AN:
0.8139
Gnomad4 FIN
AF:
0.861
AC:
0.860524
AN:
0.860524
Gnomad4 NFE
AF:
0.839
AC:
0.839064
AN:
0.839064
Gnomad4 OTH
AF:
0.846
AC:
0.845936
AN:
0.845936
Heterozygous variant carriers
0
1097
2194
3292
4389
5486
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
888
1776
2664
3552
4440
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.839
Hom.:
165824
Bravo
AF:
0.831
Asia WGS
AF:
0.816
AC:
2839
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
0.47
DANN
Benign
0.70

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: rs2542151; hg19: chr18-12779947; API