rs6883565

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 0.573 in 152,072 control chromosomes in the GnomAD database, including 27,090 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 0.57 ( 27090 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14
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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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:
0.574
AC:
87162
AN:
151954
Hom.:
27084
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.374
Gnomad AMI
AF:
0.843
Gnomad AMR
AF:
0.682
Gnomad ASJ
AF:
0.640
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.592
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.692
Gnomad OTH
AF:
0.600
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.573
AC:
87199
AN:
152072
Hom.:
27090
Cov.:
33
AF XY:
0.569
AC XY:
42324
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.373
Gnomad4 AMR
AF:
0.682
Gnomad4 ASJ
AF:
0.640
Gnomad4 EAS
AF:
0.114
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.592
Gnomad4 NFE
AF:
0.692
Gnomad4 OTH
AF:
0.603
Alfa
AF:
0.627
Hom.:
3826
Bravo
AF:
0.571
Asia WGS
AF:
0.409
AC:
1423
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.1
DANN
Benign
0.64

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: rs6883565; hg19: chr5-13600346; API