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GeneBe

rs2808630

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 0.768 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

Verdict is Benign. Variant got -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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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
Gnomad4 AMR
AF:
0.797
Gnomad4 ASJ
AF:
0.814
Gnomad4 EAS
AF:
0.819
Gnomad4 SAS
AF:
0.673
Gnomad4 FIN
AF:
0.802
Gnomad4 NFE
AF:
0.718
Gnomad4 OTH
AF:
0.775
Alfa
AF:
0.729
Hom.:
87398
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