rs1501572

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 0.398 in 151,948 control chromosomes in the GnomAD database, including 12,139 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 0.40 ( 12139 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.191
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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:
0.397
AC:
60303
AN:
151830
Hom.:
12093
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.445
Gnomad AMI
AF:
0.424
Gnomad AMR
AF:
0.342
Gnomad ASJ
AF:
0.358
Gnomad EAS
AF:
0.437
Gnomad SAS
AF:
0.425
Gnomad FIN
AF:
0.431
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.372
Gnomad OTH
AF:
0.389
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.398
AC:
60401
AN:
151948
Hom.:
12139
Cov.:
32
AF XY:
0.400
AC XY:
29739
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.446
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.358
Gnomad4 EAS
AF:
0.438
Gnomad4 SAS
AF:
0.426
Gnomad4 FIN
AF:
0.431
Gnomad4 NFE
AF:
0.372
Gnomad4 OTH
AF:
0.395
Alfa
AF:
0.375
Hom.:
1312
Bravo
AF:
0.394
Asia WGS
AF:
0.477
AC:
1659
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.8
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: rs1501572; hg19: chr9-2904794; COSMIC: COSV70237306; API