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GeneBe

rs3130695

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 0.795 in 152,008 control chromosomes in the GnomAD database, including 48,024 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 0.79 ( 48024 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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:
0.795
AC:
120730
AN:
151890
Hom.:
47987
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.810
Gnomad AMI
AF:
0.837
Gnomad AMR
AF:
0.785
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.764
Gnomad SAS
AF:
0.733
Gnomad FIN
AF:
0.808
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.786
Gnomad OTH
AF:
0.801
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.795
AC:
120816
AN:
152008
Hom.:
48024
Cov.:
31
AF XY:
0.794
AC XY:
59002
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.810
Gnomad4 AMR
AF:
0.785
Gnomad4 ASJ
AF:
0.908
Gnomad4 EAS
AF:
0.765
Gnomad4 SAS
AF:
0.731
Gnomad4 FIN
AF:
0.808
Gnomad4 NFE
AF:
0.786
Gnomad4 OTH
AF:
0.801
Alfa
AF:
0.796
Hom.:
42430
Bravo
AF:
0.793
Asia WGS
AF:
0.757
AC:
2634
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.39
Dann
Benign
0.32

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: rs3130695; hg19: chr6-31211050; API