rs8033165

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.313 in 150,274 control chromosomes in the GnomAD database, including 8,695 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 0.31 ( 8695 hom., cov: 28)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.23
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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:
0.313
AC:
46962
AN:
150158
Hom.:
8694
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.266
Gnomad EAS
AF:
0.00118
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.440
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.313
AC:
46966
AN:
150274
Hom.:
8695
Cov.:
28
AF XY:
0.306
AC XY:
22464
AN XY:
73330
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.193
Gnomad4 ASJ
AF:
0.266
Gnomad4 EAS
AF:
0.00118
Gnomad4 SAS
AF:
0.123
Gnomad4 FIN
AF:
0.496
Gnomad4 NFE
AF:
0.440
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.393
Hom.:
5282
Bravo
AF:
0.287
Asia WGS
AF:
0.100
AC:
351
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.35
CADD
Benign
23
DANN
Benign
0.87

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: rs8033165; hg19: chr15-29006093; API