rs2224572

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 0.438 in 152,006 control chromosomes in the GnomAD database, including 14,811 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 0.44 ( 14811 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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:
0.438
AC:
66481
AN:
151888
Hom.:
14785
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.480
Gnomad AMI
AF:
0.440
Gnomad AMR
AF:
0.479
Gnomad ASJ
AF:
0.477
Gnomad EAS
AF:
0.535
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.355
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.401
Gnomad OTH
AF:
0.465
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.438
AC:
66551
AN:
152006
Hom.:
14811
Cov.:
32
AF XY:
0.438
AC XY:
32563
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.480
Gnomad4 AMR
AF:
0.479
Gnomad4 ASJ
AF:
0.477
Gnomad4 EAS
AF:
0.536
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.355
Gnomad4 NFE
AF:
0.401
Gnomad4 OTH
AF:
0.470
Alfa
AF:
0.403
Hom.:
1789
Bravo
AF:
0.449
Asia WGS
AF:
0.537
AC:
1864
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.4
DANN
Benign
0.22

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: rs2224572; hg19: chr9-5288707; COSMIC: COSV60324010; API