rs1320561

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 0.514 in 152,072 control chromosomes in the GnomAD database, including 21,078 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 0.51 ( 21078 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.994
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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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:
0.514
AC:
78139
AN:
151954
Hom.:
21063
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.363
Gnomad AMI
AF:
0.782
Gnomad AMR
AF:
0.591
Gnomad ASJ
AF:
0.581
Gnomad EAS
AF:
0.532
Gnomad SAS
AF:
0.587
Gnomad FIN
AF:
0.409
Gnomad MID
AF:
0.715
Gnomad NFE
AF:
0.589
Gnomad OTH
AF:
0.563
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.514
AC:
78170
AN:
152072
Hom.:
21078
Cov.:
33
AF XY:
0.506
AC XY:
37632
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.363
Gnomad4 AMR
AF:
0.592
Gnomad4 ASJ
AF:
0.581
Gnomad4 EAS
AF:
0.532
Gnomad4 SAS
AF:
0.588
Gnomad4 FIN
AF:
0.409
Gnomad4 NFE
AF:
0.589
Gnomad4 OTH
AF:
0.565
Alfa
AF:
0.580
Hom.:
43252
Bravo
AF:
0.522
Asia WGS
AF:
0.562
AC:
1955
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.56
DANN
Benign
0.57

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: rs1320561; hg19: chr20-23097880; API