rs574666

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 0.682 in 152,040 control chromosomes in the GnomAD database, including 35,785 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 0.68 ( 35785 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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:
0.682
AC:
103611
AN:
151922
Hom.:
35774
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.643
Gnomad AMR
AF:
0.786
Gnomad ASJ
AF:
0.795
Gnomad EAS
AF:
0.972
Gnomad SAS
AF:
0.792
Gnomad FIN
AF:
0.665
Gnomad MID
AF:
0.768
Gnomad NFE
AF:
0.677
Gnomad OTH
AF:
0.713
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.682
AC:
103659
AN:
152040
Hom.:
35785
Cov.:
32
AF XY:
0.688
AC XY:
51149
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.596
Gnomad4 AMR
AF:
0.786
Gnomad4 ASJ
AF:
0.795
Gnomad4 EAS
AF:
0.972
Gnomad4 SAS
AF:
0.791
Gnomad4 FIN
AF:
0.665
Gnomad4 NFE
AF:
0.677
Gnomad4 OTH
AF:
0.718
Alfa
AF:
0.677
Hom.:
4490
Bravo
AF:
0.690
Asia WGS
AF:
0.858
AC:
2982
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
6.0
DANN
Benign
0.73

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: rs574666; hg19: chr4-20236850; COSMIC: COSV53465233; API