rs3091244

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 0.3 in 151,984 control chromosomes in the GnomAD database, including 7,034 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 ( 7034 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.68
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=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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:
0.300
AC:
45553
AN:
151866
Hom.:
7036
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.291
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.319
Gnomad ASJ
AF:
0.305
Gnomad EAS
AF:
0.0616
Gnomad SAS
AF:
0.244
Gnomad FIN
AF:
0.355
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.300
AC:
45581
AN:
151984
Hom.:
7034
Cov.:
30
AF XY:
0.299
AC XY:
22217
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.291
AC:
0.290727
AN:
0.290727
Gnomad4 AMR
AF:
0.319
AC:
0.318955
AN:
0.318955
Gnomad4 ASJ
AF:
0.305
AC:
0.305187
AN:
0.305187
Gnomad4 EAS
AF:
0.0616
AC:
0.0615534
AN:
0.0615534
Gnomad4 SAS
AF:
0.246
AC:
0.245538
AN:
0.245538
Gnomad4 FIN
AF:
0.355
AC:
0.354585
AN:
0.354585
Gnomad4 NFE
AF:
0.314
AC:
0.3142
AN:
0.3142
Gnomad4 OTH
AF:
0.292
AC:
0.291864
AN:
0.291864
Heterozygous variant carriers
0
1590
3180
4770
6360
7950
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
456
912
1368
1824
2280
<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:
0.380
Hom.:
12835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.053
DANN
Benign
0.67

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: rs3091244; hg19: chr1-159684665; API