rs1565863

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 0.563 in 152,080 control chromosomes in the GnomAD database, including 26,339 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 0.56 ( 26339 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.770
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 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:
0.563
AC:
85565
AN:
151962
Hom.:
26335
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.330
Gnomad AMI
AF:
0.843
Gnomad AMR
AF:
0.570
Gnomad ASJ
AF:
0.589
Gnomad EAS
AF:
0.268
Gnomad SAS
AF:
0.517
Gnomad FIN
AF:
0.700
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.704
Gnomad OTH
AF:
0.535
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.563
AC:
85599
AN:
152080
Hom.:
26339
Cov.:
32
AF XY:
0.560
AC XY:
41628
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.329
Gnomad4 AMR
AF:
0.570
Gnomad4 ASJ
AF:
0.589
Gnomad4 EAS
AF:
0.268
Gnomad4 SAS
AF:
0.518
Gnomad4 FIN
AF:
0.700
Gnomad4 NFE
AF:
0.704
Gnomad4 OTH
AF:
0.537
Alfa
AF:
0.670
Hom.:
56093
Bravo
AF:
0.542
Asia WGS
AF:
0.381
AC:
1327
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.44
DANN
Benign
0.38

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: rs1565863; hg19: chr15-40438120; API