rs79703820

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 0.02 in 152,332 control chromosomes in the GnomAD database, including 58 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 0.020 ( 58 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.741
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0597 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:
0.0200
AC:
3044
AN:
152214
Hom.:
58
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00567
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0164
Gnomad ASJ
AF:
0.0712
Gnomad EAS
AF:
0.00250
Gnomad SAS
AF:
0.0648
Gnomad FIN
AF:
0.0106
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0259
Gnomad OTH
AF:
0.0301
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0200
AC:
3047
AN:
152332
Hom.:
58
Cov.:
32
AF XY:
0.0208
AC XY:
1548
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.00568
Gnomad4 AMR
AF:
0.0163
Gnomad4 ASJ
AF:
0.0712
Gnomad4 EAS
AF:
0.00251
Gnomad4 SAS
AF:
0.0657
Gnomad4 FIN
AF:
0.0106
Gnomad4 NFE
AF:
0.0259
Gnomad4 OTH
AF:
0.0298
Alfa
AF:
0.00958
Hom.:
0
Bravo
AF:
0.0193
Asia WGS
AF:
0.0320
AC:
110
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
7.5
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: rs79703820; hg19: chr9-24769088; API