rs723511

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 0.591 in 151,964 control chromosomes in the GnomAD database, including 28,090 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 0.59 ( 28090 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.77
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.591
AC:
89680
AN:
151846
Hom.:
28038
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.804
Gnomad AMI
AF:
0.368
Gnomad AMR
AF:
0.552
Gnomad ASJ
AF:
0.548
Gnomad EAS
AF:
0.743
Gnomad SAS
AF:
0.530
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.671
Gnomad NFE
AF:
0.489
Gnomad OTH
AF:
0.576
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.591
AC:
89796
AN:
151964
Hom.:
28090
Cov.:
32
AF XY:
0.587
AC XY:
43628
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.804
Gnomad4 AMR
AF:
0.553
Gnomad4 ASJ
AF:
0.548
Gnomad4 EAS
AF:
0.743
Gnomad4 SAS
AF:
0.530
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.489
Gnomad4 OTH
AF:
0.580
Alfa
AF:
0.521
Hom.:
10280
Bravo
AF:
0.609
Asia WGS
AF:
0.650
AC:
2263
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.0010
DANN
Benign
0.37

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: rs723511; hg19: chr20-6838358; API