rs2569360

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 0.375 in 151,876 control chromosomes in the GnomAD database, including 11,289 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 0.37 ( 11289 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.375
AC:
56909
AN:
151756
Hom.:
11285
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.473
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.387
Gnomad SAS
AF:
0.432
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.439
Gnomad OTH
AF:
0.421
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.375
AC:
56921
AN:
151876
Hom.:
11289
Cov.:
31
AF XY:
0.372
AC XY:
27614
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.232
Gnomad4 AMR
AF:
0.386
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.386
Gnomad4 SAS
AF:
0.433
Gnomad4 FIN
AF:
0.404
Gnomad4 NFE
AF:
0.440
Gnomad4 OTH
AF:
0.419
Alfa
AF:
0.394
Hom.:
1509
Bravo
AF:
0.371
Asia WGS
AF:
0.385
AC:
1342
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.8
DANN
Benign
0.71

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: rs2569360; hg19: chr10-78588745; API