rs2023794

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 0.0609 in 152,274 control chromosomes in the GnomAD database, including 410 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 0.061 ( 410 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.00
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=-0.44).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 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:
0.0610
AC:
9280
AN:
152154
Hom.:
411
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0161
Gnomad AMI
AF:
0.0110
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.0415
Gnomad EAS
AF:
0.0808
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.0497
Gnomad MID
AF:
0.0510
Gnomad NFE
AF:
0.0678
Gnomad OTH
AF:
0.0664
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0609
AC:
9281
AN:
152274
Hom.:
410
Cov.:
32
AF XY:
0.0625
AC XY:
4651
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.0161
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.0415
Gnomad4 EAS
AF:
0.0804
Gnomad4 SAS
AF:
0.129
Gnomad4 FIN
AF:
0.0497
Gnomad4 NFE
AF:
0.0678
Gnomad4 OTH
AF:
0.0658
Alfa
AF:
0.0695
Hom.:
93
Bravo
AF:
0.0663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
17
DANN
Benign
0.81

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: rs2023794; hg19: chr17-41837660; API