rs1572372

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 0.354 in 152,022 control chromosomes in the GnomAD database, including 10,253 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 0.35 ( 10253 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.832
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=-0.69).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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:
0.354
AC:
53768
AN:
151904
Hom.:
10242
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.207
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.363
Gnomad ASJ
AF:
0.356
Gnomad EAS
AF:
0.363
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.433
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.365
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.354
AC:
53814
AN:
152022
Hom.:
10253
Cov.:
32
AF XY:
0.358
AC XY:
26567
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.207
Gnomad4 AMR
AF:
0.363
Gnomad4 ASJ
AF:
0.356
Gnomad4 EAS
AF:
0.363
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.433
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.366
Alfa
AF:
0.400
Hom.:
5922
Bravo
AF:
0.338
Asia WGS
AF:
0.446
AC:
1548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
8.8
DANN
Benign
0.77

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: rs1572372; hg19: chr13-20840004; API