GeneBe

rs9610271

Variant names:

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 0.292 in 152,110 control chromosomes in the GnomAD database, including 7,282 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 0.29 ( 7280 hom., cov: 32)
Exomes 𝑓: 0.31 ( 2 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.740

Publications

11 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 = 0.378 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:
0.292
AC:
44388
AN:
151940
Hom.:
7280
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.382
Gnomad AMR
AF:
0.302
Gnomad ASJ
AF:
0.441
Gnomad EAS
AF:
0.100
Gnomad SAS
AF:
0.209
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.382
Gnomad OTH
AF:
0.345
GnomAD4 exome
AF:
0.308
AC:
16
AN:
52
Hom.:
2
Cov.:
0
AF XY:
0.222
AC XY:
8
AN XY:
36
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.326
AC:
15
AN:
46
Other (OTH)
AF:
0.500
AC:
1
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.563
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.292
AC:
44395
AN:
152058
Hom.:
7280
Cov.:
32
AF XY:
0.284
AC XY:
21141
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.164
AC:
6811
AN:
41486
American (AMR)
AF:
0.302
AC:
4607
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.441
AC:
1528
AN:
3468
East Asian (EAS)
AF:
0.100
AC:
520
AN:
5182
South Asian (SAS)
AF:
0.210
AC:
1011
AN:
4818
European-Finnish (FIN)
AF:
0.263
AC:
2782
AN:
10560
Middle Eastern (MID)
AF:
0.422
AC:
124
AN:
294
European-Non Finnish (NFE)
AF:
0.382
AC:
25945
AN:
67956
Other (OTH)
AF:
0.341
AC:
719
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1552
3104
4657
6209
7761
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
438
876
1314
1752
2190
<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:
0.358
Hom.:
13003
Bravo
AF:
0.290
Asia WGS
AF:
0.152
AC:
530
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
1.1
DANN
Benign
0.52
PhyloP100
-0.74
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs9610271; hg19: chr22-22112527; API