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GeneBe

rs817097

Positions:

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 0.357 in 151,370 control chromosomes in the GnomAD database, including 10,100 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 0.36 ( 10100 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.182
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.357
AC:
53936
AN:
151268
Hom.:
10093
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.459
Gnomad AMI
AF:
0.336
Gnomad AMR
AF:
0.272
Gnomad ASJ
AF:
0.340
Gnomad EAS
AF:
0.143
Gnomad SAS
AF:
0.271
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.325
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.368
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.357
AC:
53976
AN:
151370
Hom.:
10100
Cov.:
31
AF XY:
0.351
AC XY:
25945
AN XY:
73938
show subpopulations
Gnomad4 AFR
AF:
0.459
Gnomad4 AMR
AF:
0.271
Gnomad4 ASJ
AF:
0.340
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.271
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.348
Gnomad4 OTH
AF:
0.367
Alfa
AF:
0.343
Hom.:
17412
Bravo
AF:
0.359
Asia WGS
AF:
0.263
AC:
916
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
1.4
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: rs817097; hg19: chr17-67378062; API