rs3918242

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 0.137 in 151,998 control chromosomes in the GnomAD database, including 1,511 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 0.14 ( 1511 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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:
0.137
AC:
20853
AN:
151880
Hom.:
1511
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.121
Gnomad AMI
AF:
0.0800
Gnomad AMR
AF:
0.0896
Gnomad ASJ
AF:
0.156
Gnomad EAS
AF:
0.141
Gnomad SAS
AF:
0.226
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.134
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20867
AN:
151998
Hom.:
1511
Cov.:
32
AF XY:
0.138
AC XY:
10246
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.121
Gnomad4 AMR
AF:
0.0894
Gnomad4 ASJ
AF:
0.156
Gnomad4 EAS
AF:
0.141
Gnomad4 SAS
AF:
0.225
Gnomad4 FIN
AF:
0.171
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.174
Hom.:
474
Bravo
AF:
0.128
Asia WGS
AF:
0.177
AC:
614
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
3.7
DANN
Benign
0.56

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: rs3918242; hg19: chr20-44635976; API