rs580628

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 0.071 in 111,134 control chromosomes in the GnomAD database, including 242 homozygotes. There are 2,462 hemizygotes in GnomAD. 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 0.071 ( 242 hom., 2462 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.835
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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0914 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:
0.0710
AC:
7890
AN:
111090
Hom.:
241
Cov.:
23
AF XY:
0.0739
AC XY:
2461
AN XY:
33304
show subpopulations
Gnomad AFR
AF:
0.0174
Gnomad AMI
AF:
0.0513
Gnomad AMR
AF:
0.0786
Gnomad ASJ
AF:
0.0928
Gnomad EAS
AF:
0.0279
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.148
Gnomad NFE
AF:
0.0917
Gnomad OTH
AF:
0.0866
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0710
AC:
7888
AN:
111134
Hom.:
242
Cov.:
23
AF XY:
0.0738
AC XY:
2462
AN XY:
33358
show subpopulations
Gnomad4 AFR
AF:
0.0174
Gnomad4 AMR
AF:
0.0785
Gnomad4 ASJ
AF:
0.0928
Gnomad4 EAS
AF:
0.0277
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.0917
Gnomad4 OTH
AF:
0.0855
Alfa
AF:
0.0886
Hom.:
3399
Bravo
AF:
0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.7
DANN
Benign
0.67

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: rs580628; hg19: chrX-144442552; API