rs739750

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 0.14 in 152,178 control chromosomes in the GnomAD database, including 1,846 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 0.14 ( 1846 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

Publications

1 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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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:
0.139
AC:
21186
AN:
152060
Hom.:
1832
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.150
Gnomad AMR
AF:
0.175
Gnomad ASJ
AF:
0.0559
Gnomad EAS
AF:
0.182
Gnomad SAS
AF:
0.0710
Gnomad FIN
AF:
0.100
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0849
Gnomad OTH
AF:
0.127
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.140
AC:
21247
AN:
152178
Hom.:
1846
Cov.:
32
AF XY:
0.141
AC XY:
10507
AN XY:
74422
show subpopulations
African (AFR)
AF:
0.237
AC:
9813
AN:
41492
American (AMR)
AF:
0.176
AC:
2692
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.0559
AC:
194
AN:
3470
East Asian (EAS)
AF:
0.183
AC:
942
AN:
5160
South Asian (SAS)
AF:
0.0711
AC:
343
AN:
4824
European-Finnish (FIN)
AF:
0.100
AC:
1062
AN:
10606
Middle Eastern (MID)
AF:
0.0714
AC:
21
AN:
294
European-Non Finnish (NFE)
AF:
0.0849
AC:
5771
AN:
68010
Other (OTH)
AF:
0.129
AC:
272
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
880
1760
2639
3519
4399
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
214
428
642
856
1070
<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:
0.101
Hom.:
1671
Bravo
AF:
0.153
Asia WGS
AF:
0.146
AC:
505
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.2
DANN
Benign
0.58
PhyloP100
0.26

Splicing

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

Publications

Other links and lift over

dbSNP: rs739750; hg19: chr7-25262364; API