rs9263969

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 0.219 in 151,964 control chromosomes in the GnomAD database, including 3,927 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 0.22 ( 3927 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48
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=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

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:
0.219
AC:
33185
AN:
151848
Hom.:
3924
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.256
Gnomad ASJ
AF:
0.422
Gnomad EAS
AF:
0.125
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.237
Gnomad OTH
AF:
0.274
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33208
AN:
151964
Hom.:
3927
Cov.:
33
AF XY:
0.221
AC XY:
16405
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.148
Gnomad4 AMR
AF:
0.256
Gnomad4 ASJ
AF:
0.422
Gnomad4 EAS
AF:
0.125
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.237
Gnomad4 OTH
AF:
0.274
Alfa
AF:
0.246
Hom.:
3149
Bravo
AF:
0.217
Asia WGS
AF:
0.193
AC:
671
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
3.2
DANN
Benign
0.31

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: rs9263969; hg19: chr6-31186534; API