GeneBe

5-177313243-A-G

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 0.726 in 984,646 control chromosomes in the GnomAD database, including 260,002 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 0.70 ( 37447 hom., cov: 31)
Exomes 𝑓: 0.73 ( 222555 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

34 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 (AMR) allele frequency at 95% confidence interval = 0.729 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:
0.700
AC:
106104
AN:
151598
Hom.:
37442
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.648
Gnomad AMI
AF:
0.844
Gnomad AMR
AF:
0.737
Gnomad ASJ
AF:
0.817
Gnomad EAS
AF:
0.453
Gnomad SAS
AF:
0.654
Gnomad FIN
AF:
0.709
Gnomad MID
AF:
0.842
Gnomad NFE
AF:
0.734
Gnomad OTH
AF:
0.738
GnomAD4 exome
AF:
0.730
AC:
608271
AN:
832934
Hom.:
222555
Cov.:
39
AF XY:
0.731
AC XY:
281157
AN XY:
384648
show subpopulations
African (AFR)
AF:
0.642
AC:
10126
AN:
15778
American (AMR)
AF:
0.724
AC:
712
AN:
984
Ashkenazi Jewish (ASJ)
AF:
0.819
AC:
4217
AN:
5150
East Asian (EAS)
AF:
0.438
AC:
1588
AN:
3626
South Asian (SAS)
AF:
0.694
AC:
11416
AN:
16458
European-Finnish (FIN)
AF:
0.696
AC:
192
AN:
276
Middle Eastern (MID)
AF:
0.773
AC:
1253
AN:
1620
European-Non Finnish (NFE)
AF:
0.734
AC:
559500
AN:
761754
Other (OTH)
AF:
0.706
AC:
19267
AN:
27288
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.459
Heterozygous variant carriers
0
8714
17428
26143
34857
43571
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
18828
37656
56484
75312
94140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.700
AC:
106156
AN:
151712
Hom.:
37447
Cov.:
31
AF XY:
0.697
AC XY:
51626
AN XY:
74098
show subpopulations
African (AFR)
AF:
0.647
AC:
26751
AN:
41320
American (AMR)
AF:
0.737
AC:
11255
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.817
AC:
2833
AN:
3468
East Asian (EAS)
AF:
0.453
AC:
2336
AN:
5156
South Asian (SAS)
AF:
0.653
AC:
3139
AN:
4808
European-Finnish (FIN)
AF:
0.709
AC:
7398
AN:
10428
Middle Eastern (MID)
AF:
0.837
AC:
246
AN:
294
European-Non Finnish (NFE)
AF:
0.734
AC:
49885
AN:
67946
Other (OTH)
AF:
0.735
AC:
1543
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
1614
3228
4841
6455
8069
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
824
1648
2472
3296
4120
<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:
0.721
Hom.:
102322
Bravo
AF:
0.700
Asia WGS
AF:
0.538
AC:
1876
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
0.26
DANN
Benign
0.71
PhyloP100
-1.5
PromoterAI
0.014
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs11949767; hg19: chr5-176740244; API