1-91656775-A-C

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 0.736 in 152,142 control chromosomes in the GnomAD database, including 41,967 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 0.74 ( 41967 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.344

Publications

4 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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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:
0.736
AC:
111857
AN:
152022
Hom.:
41951
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.594
Gnomad AMI
AF:
0.803
Gnomad AMR
AF:
0.659
Gnomad ASJ
AF:
0.803
Gnomad EAS
AF:
0.919
Gnomad SAS
AF:
0.797
Gnomad FIN
AF:
0.899
Gnomad MID
AF:
0.744
Gnomad NFE
AF:
0.791
Gnomad OTH
AF:
0.737
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.736
AC:
111921
AN:
152142
Hom.:
41967
Cov.:
32
AF XY:
0.740
AC XY:
55062
AN XY:
74384
show subpopulations
African (AFR)
AF:
0.594
AC:
24636
AN:
41472
American (AMR)
AF:
0.659
AC:
10072
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.803
AC:
2782
AN:
3466
East Asian (EAS)
AF:
0.918
AC:
4752
AN:
5174
South Asian (SAS)
AF:
0.796
AC:
3838
AN:
4820
European-Finnish (FIN)
AF:
0.899
AC:
9531
AN:
10600
Middle Eastern (MID)
AF:
0.738
AC:
217
AN:
294
European-Non Finnish (NFE)
AF:
0.791
AC:
53808
AN:
68004
Other (OTH)
AF:
0.735
AC:
1553
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1461
2922
4384
5845
7306
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
850
1700
2550
3400
4250
<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:
0.764
Hom.:
140250
Bravo
AF:
0.711
Asia WGS
AF:
0.844
AC:
2933
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
9.0
DANN
Benign
0.73
PhyloP100
0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs2148322; hg19: chr1-92122332; API