rs1347851

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 0.807 in 151,934 control chromosomes in the GnomAD database, including 49,708 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 0.81 ( 49708 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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:
0.808
AC:
122593
AN:
151816
Hom.:
49669
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.866
Gnomad AMI
AF:
0.793
Gnomad AMR
AF:
0.735
Gnomad ASJ
AF:
0.813
Gnomad EAS
AF:
0.879
Gnomad SAS
AF:
0.820
Gnomad FIN
AF:
0.823
Gnomad MID
AF:
0.741
Gnomad NFE
AF:
0.780
Gnomad OTH
AF:
0.796
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.807
AC:
122684
AN:
151934
Hom.:
49708
Cov.:
31
AF XY:
0.810
AC XY:
60138
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.867
Gnomad4 AMR
AF:
0.734
Gnomad4 ASJ
AF:
0.813
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.820
Gnomad4 FIN
AF:
0.823
Gnomad4 NFE
AF:
0.780
Gnomad4 OTH
AF:
0.793
Alfa
AF:
0.792
Hom.:
23846
Bravo
AF:
0.802
Asia WGS
AF:
0.810
AC:
2818
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.066
DANN
Benign
0.23

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: rs1347851; hg19: chr12-90566978; API