rs1868841

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 0.614 in 151,886 control chromosomes in the GnomAD database, including 30,835 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 0.61 ( 30835 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.601
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 = 0.862 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:
0.613
AC:
93092
AN:
151768
Hom.:
30775
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.869
Gnomad AMI
AF:
0.567
Gnomad AMR
AF:
0.544
Gnomad ASJ
AF:
0.565
Gnomad EAS
AF:
0.715
Gnomad SAS
AF:
0.654
Gnomad FIN
AF:
0.501
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.485
Gnomad OTH
AF:
0.592
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.614
AC:
93213
AN:
151886
Hom.:
30835
Cov.:
33
AF XY:
0.614
AC XY:
45626
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.869
Gnomad4 AMR
AF:
0.544
Gnomad4 ASJ
AF:
0.565
Gnomad4 EAS
AF:
0.715
Gnomad4 SAS
AF:
0.653
Gnomad4 FIN
AF:
0.501
Gnomad4 NFE
AF:
0.485
Gnomad4 OTH
AF:
0.596
Alfa
AF:
0.515
Hom.:
27822
Bravo
AF:
0.623
Asia WGS
AF:
0.689
AC:
2398
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.10
DANN
Benign
0.42

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: rs1868841; hg19: chr8-58364003; API