rs508865

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.65 ( 16510 hom., 20996 hem., cov: 23)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.159
Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.650
AC:
71436
AN:
109956
Hom.:
16517
Cov.:
23
AF XY:
0.650
AC XY:
20982
AN XY:
32262
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.789
Gnomad AMR
AF:
0.645
Gnomad ASJ
AF:
0.632
Gnomad EAS
AF:
0.834
Gnomad SAS
AF:
0.617
Gnomad FIN
AF:
0.728
Gnomad MID
AF:
0.634
Gnomad NFE
AF:
0.661
Gnomad OTH
AF:
0.676
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.649
AC:
71437
AN:
110006
Hom.:
16510
Cov.:
23
AF XY:
0.650
AC XY:
20996
AN XY:
32322
show subpopulations
Gnomad4 AFR
AF:
0.595
Gnomad4 AMR
AF:
0.644
Gnomad4 ASJ
AF:
0.632
Gnomad4 EAS
AF:
0.833
Gnomad4 SAS
AF:
0.618
Gnomad4 FIN
AF:
0.728
Gnomad4 NFE
AF:
0.661
Gnomad4 OTH
AF:
0.677
Alfa
AF:
0.653
Hom.:
5755
Bravo
AF:
0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.65

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: rs508865; hg19: chrX-113814115; API