rs1851024

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 0.928 in 152,150 control chromosomes in the GnomAD database, including 65,798 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 0.93 ( 65798 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179
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=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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:
0.928
AC:
141087
AN:
152032
Hom.:
65772
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.837
Gnomad AMI
AF:
0.999
Gnomad AMR
AF:
0.945
Gnomad ASJ
AF:
0.979
Gnomad EAS
AF:
0.834
Gnomad SAS
AF:
0.922
Gnomad FIN
AF:
0.950
Gnomad MID
AF:
0.956
Gnomad NFE
AF:
0.980
Gnomad OTH
AF:
0.935
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.928
AC:
141168
AN:
152150
Hom.:
65798
Cov.:
31
AF XY:
0.927
AC XY:
68927
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.837
Gnomad4 AMR
AF:
0.945
Gnomad4 ASJ
AF:
0.979
Gnomad4 EAS
AF:
0.834
Gnomad4 SAS
AF:
0.921
Gnomad4 FIN
AF:
0.950
Gnomad4 NFE
AF:
0.980
Gnomad4 OTH
AF:
0.934
Alfa
AF:
0.969
Hom.:
142831
Bravo
AF:
0.922
Asia WGS
AF:
0.836
AC:
2909
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.90
DANN
Benign
0.50

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: rs1851024; hg19: chr4-72707821; API