GeneBe

16-56960616-C-T

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 0.289 in 480,014 control chromosomes in the GnomAD database, including 21,163 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 0.26 ( 5583 hom., cov: 32)
Exomes 𝑓: 0.30 ( 15580 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.671

Publications

78 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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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:
0.258
AC:
39182
AN:
151978
Hom.:
5583
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.144
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.253
Gnomad EAS
AF:
0.167
Gnomad SAS
AF:
0.334
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.245
Gnomad NFE
AF:
0.322
Gnomad OTH
AF:
0.248
GnomAD2 exomes
AF:
0.285
AC:
48146
AN:
168940
AF XY:
0.292
show subpopulations
Gnomad AFR exome
AF:
0.132
Gnomad AMR exome
AF:
0.309
Gnomad ASJ exome
AF:
0.261
Gnomad EAS exome
AF:
0.159
Gnomad FIN exome
AF:
0.265
Gnomad NFE exome
AF:
0.310
Gnomad OTH exome
AF:
0.289
GnomAD4 exome
AF:
0.303
AC:
99410
AN:
327918
Hom.:
15580
Cov.:
0
AF XY:
0.307
AC XY:
57511
AN XY:
187072
show subpopulations
African (AFR)
AF:
0.138
AC:
1326
AN:
9598
American (AMR)
AF:
0.311
AC:
9348
AN:
30022
Ashkenazi Jewish (ASJ)
AF:
0.260
AC:
2872
AN:
11038
East Asian (EAS)
AF:
0.162
AC:
1821
AN:
11246
South Asian (SAS)
AF:
0.335
AC:
20567
AN:
61316
European-Finnish (FIN)
AF:
0.273
AC:
3912
AN:
14322
Middle Eastern (MID)
AF:
0.264
AC:
740
AN:
2808
European-Non Finnish (NFE)
AF:
0.316
AC:
54483
AN:
172358
Other (OTH)
AF:
0.285
AC:
4341
AN:
15210
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.441
Heterozygous variant carriers
0
3963
7927
11890
15854
19817
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
370
740
1110
1480
1850
<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:
0.258
AC:
39182
AN:
152096
Hom.:
5583
Cov.:
32
AF XY:
0.257
AC XY:
19116
AN XY:
74352
show subpopulations
African (AFR)
AF:
0.143
AC:
5947
AN:
41492
American (AMR)
AF:
0.269
AC:
4118
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.253
AC:
878
AN:
3470
East Asian (EAS)
AF:
0.167
AC:
861
AN:
5170
South Asian (SAS)
AF:
0.336
AC:
1621
AN:
4826
European-Finnish (FIN)
AF:
0.276
AC:
2916
AN:
10570
Middle Eastern (MID)
AF:
0.236
AC:
69
AN:
292
European-Non Finnish (NFE)
AF:
0.322
AC:
21902
AN:
67950
Other (OTH)
AF:
0.244
AC:
516
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1444
2888
4332
5776
7220
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
418
836
1254
1672
2090
<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:
0.286
Hom.:
10081
Bravo
AF:
0.251
Asia WGS
AF:
0.217
AC:
756
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.2
DANN
Benign
0.73
PhyloP100
-0.67

Splicing

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

Publications

Other links and lift over

dbSNP: rs17231506; hg19: chr16-56994528; COSMIC: COSV52364891; API