rs480110

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 0.398 in 152,014 control chromosomes in the GnomAD database, including 14,150 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 ( 14150 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.432

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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:
0.398
AC:
60478
AN:
151896
Hom.:
14150
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.488
Gnomad AMR
AF:
0.406
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.221
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.556
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.532
Gnomad OTH
AF:
0.402
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.398
AC:
60480
AN:
152014
Hom.:
14150
Cov.:
32
AF XY:
0.395
AC XY:
29345
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.166
AC:
6872
AN:
41482
American (AMR)
AF:
0.405
AC:
6188
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.408
AC:
1417
AN:
3472
East Asian (EAS)
AF:
0.219
AC:
1134
AN:
5174
South Asian (SAS)
AF:
0.293
AC:
1406
AN:
4800
European-Finnish (FIN)
AF:
0.556
AC:
5870
AN:
10560
Middle Eastern (MID)
AF:
0.429
AC:
126
AN:
294
European-Non Finnish (NFE)
AF:
0.532
AC:
36174
AN:
67950
Other (OTH)
AF:
0.402
AC:
848
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1689
3378
5068
6757
8446
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
560
1120
1680
2240
2800
<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:
0.489
Hom.:
11693
Bravo
AF:
0.380
Asia WGS
AF:
0.287
AC:
998
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.33
DANN
Benign
0.82
PhyloP100
-0.43

Splicing

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

Publications

Other links and lift over

dbSNP: rs480110; hg19: chr6-145406034; COSMIC: COSV60289952; API