rs4856162

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 0.423 in 151,742 control chromosomes in the GnomAD database, including 15,225 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 0.42 ( 15225 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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:
0.423
AC:
64114
AN:
151622
Hom.:
15172
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.637
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.445
Gnomad ASJ
AF:
0.351
Gnomad EAS
AF:
0.493
Gnomad SAS
AF:
0.476
Gnomad FIN
AF:
0.375
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.292
Gnomad OTH
AF:
0.429
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64237
AN:
151742
Hom.:
15225
Cov.:
32
AF XY:
0.431
AC XY:
31970
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.637
Gnomad4 AMR
AF:
0.445
Gnomad4 ASJ
AF:
0.351
Gnomad4 EAS
AF:
0.493
Gnomad4 SAS
AF:
0.478
Gnomad4 FIN
AF:
0.375
Gnomad4 NFE
AF:
0.292
Gnomad4 OTH
AF:
0.434
Alfa
AF:
0.331
Hom.:
8892
Bravo
AF:
0.438
Asia WGS
AF:
0.543
AC:
1887
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.7
DANN
Benign
0.49

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: rs4856162; hg19: chr3-103292226; API