rs665579

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.222 in 152,068 control chromosomes in the GnomAD database, including 3,741 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 0.22 ( 3741 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.500

Publications

2 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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:
0.222
AC:
33733
AN:
151950
Hom.:
3734
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.144
Gnomad AMR
AF:
0.227
Gnomad ASJ
AF:
0.279
Gnomad EAS
AF:
0.118
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.190
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.232
Gnomad OTH
AF:
0.228
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.222
AC:
33751
AN:
152068
Hom.:
3741
Cov.:
32
AF XY:
0.220
AC XY:
16326
AN XY:
74348
show subpopulations
African (AFR)
AF:
0.220
AC:
9107
AN:
41488
American (AMR)
AF:
0.228
AC:
3477
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.279
AC:
966
AN:
3466
East Asian (EAS)
AF:
0.117
AC:
607
AN:
5170
South Asian (SAS)
AF:
0.234
AC:
1127
AN:
4814
European-Finnish (FIN)
AF:
0.190
AC:
2013
AN:
10594
Middle Eastern (MID)
AF:
0.296
AC:
87
AN:
294
European-Non Finnish (NFE)
AF:
0.232
AC:
15759
AN:
67964
Other (OTH)
AF:
0.226
AC:
477
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1365
2729
4094
5458
6823
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
368
736
1104
1472
1840
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.232
Hom.:
11618
Bravo
AF:
0.223
Asia WGS
AF:
0.187
AC:
655
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.72
DANN
Benign
0.55
PhyloP100
-0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs665579; hg19: chr5-62811418; API