chr5-105644654-T-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 0.643 in 151,924 control chromosomes in the GnomAD database, including 31,971 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 0.64 ( 31971 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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:
0.643
AC:
97551
AN:
151806
Hom.:
31920
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.713
Gnomad AMI
AF:
0.567
Gnomad AMR
AF:
0.696
Gnomad ASJ
AF:
0.633
Gnomad EAS
AF:
0.319
Gnomad SAS
AF:
0.669
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.669
Gnomad NFE
AF:
0.632
Gnomad OTH
AF:
0.658
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.643
AC:
97665
AN:
151924
Hom.:
31971
Cov.:
32
AF XY:
0.637
AC XY:
47284
AN XY:
74252
show subpopulations
African (AFR)
AF:
0.713
AC:
29566
AN:
41456
American (AMR)
AF:
0.697
AC:
10631
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.633
AC:
2195
AN:
3468
East Asian (EAS)
AF:
0.318
AC:
1641
AN:
5154
South Asian (SAS)
AF:
0.669
AC:
3225
AN:
4820
European-Finnish (FIN)
AF:
0.513
AC:
5411
AN:
10540
Middle Eastern (MID)
AF:
0.658
AC:
192
AN:
292
European-Non Finnish (NFE)
AF:
0.632
AC:
42904
AN:
67916
Other (OTH)
AF:
0.656
AC:
1384
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1746
3492
5239
6985
8731
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
790
1580
2370
3160
3950
<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:
0.639
Hom.:
131123
Bravo
AF:
0.655
Asia WGS
AF:
0.532
AC:
1851
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.5
DANN
Benign
0.84
PhyloP100
-0.38

Splicing

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

Publications

Other links and lift over

dbSNP: rs6872786; hg19: chr5-104980355; API