rs2808630

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 0.768 in 152,164 control chromosomes in the GnomAD database, including 45,128 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 0.77 ( 45128 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.437
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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:
0.768
AC:
116795
AN:
152046
Hom.:
45080
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.835
Gnomad AMI
AF:
0.632
Gnomad AMR
AF:
0.796
Gnomad ASJ
AF:
0.814
Gnomad EAS
AF:
0.820
Gnomad SAS
AF:
0.671
Gnomad FIN
AF:
0.802
Gnomad MID
AF:
0.753
Gnomad NFE
AF:
0.718
Gnomad OTH
AF:
0.775
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.768
AC:
116903
AN:
152164
Hom.:
45128
Cov.:
32
AF XY:
0.770
AC XY:
57307
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.835
AC:
0.834601
AN:
0.834601
Gnomad4 AMR
AF:
0.797
AC:
0.796601
AN:
0.796601
Gnomad4 ASJ
AF:
0.814
AC:
0.814228
AN:
0.814228
Gnomad4 EAS
AF:
0.819
AC:
0.818902
AN:
0.818902
Gnomad4 SAS
AF:
0.673
AC:
0.67255
AN:
0.67255
Gnomad4 FIN
AF:
0.802
AC:
0.801969
AN:
0.801969
Gnomad4 NFE
AF:
0.718
AC:
0.718385
AN:
0.718385
Gnomad4 OTH
AF:
0.775
AC:
0.774834
AN:
0.774834
Heterozygous variant carriers
0
1388
2777
4165
5554
6942
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
860
1720
2580
3440
4300
<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:
0.733
Hom.:
172362
Bravo
AF:
0.773
Asia WGS
AF:
0.741
AC:
2578
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.3
DANN
Benign
0.47

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: rs2808630; hg19: chr1-159680868; API