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GeneBe

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:

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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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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