GeneBe

chr7-142666251-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 0.127 in 168,298 control chromosomes in the GnomAD database, including 1,617 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 0.13 ( 1463 hom., cov: 29)
Exomes 𝑓: 0.12 ( 154 hom. )

Consequence

TRB
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.374

Publications

1 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BA1
GnomAd4 highest subpopulation (EAS) 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
TRB n.142666251A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.127
AC:
19305
AN:
151674
Hom.:
1461
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.108
Gnomad AMR
AF:
0.180
Gnomad ASJ
AF:
0.0629
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.0721
Gnomad FIN
AF:
0.0991
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0839
Gnomad OTH
AF:
0.124
GnomAD4 exome
AF:
0.120
AC:
1986
AN:
16504
Hom.:
154
Cov.:
0
AF XY:
0.117
AC XY:
1033
AN XY:
8824
show subpopulations
African (AFR)
AF:
0.192
AC:
83
AN:
432
American (AMR)
AF:
0.218
AC:
111
AN:
510
Ashkenazi Jewish (ASJ)
AF:
0.0793
AC:
53
AN:
668
East Asian (EAS)
AF:
0.283
AC:
420
AN:
1482
South Asian (SAS)
AF:
0.0372
AC:
7
AN:
188
European-Finnish (FIN)
AF:
0.111
AC:
146
AN:
1316
Middle Eastern (MID)
AF:
0.125
AC:
10
AN:
80
European-Non Finnish (NFE)
AF:
0.0953
AC:
1023
AN:
10730
Other (OTH)
AF:
0.121
AC:
133
AN:
1098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
85
170
255
340
425
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
10
20
30
40
50
<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:
0.127
AC:
19345
AN:
151794
Hom.:
1463
Cov.:
29
AF XY:
0.128
AC XY:
9509
AN XY:
74192
show subpopulations
African (AFR)
AF:
0.185
AC:
7648
AN:
41332
American (AMR)
AF:
0.180
AC:
2737
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
0.0629
AC:
218
AN:
3468
East Asian (EAS)
AF:
0.244
AC:
1256
AN:
5150
South Asian (SAS)
AF:
0.0728
AC:
350
AN:
4808
European-Finnish (FIN)
AF:
0.0991
AC:
1047
AN:
10568
Middle Eastern (MID)
AF:
0.119
AC:
35
AN:
294
European-Non Finnish (NFE)
AF:
0.0839
AC:
5698
AN:
67944
Other (OTH)
AF:
0.123
AC:
258
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
793
1587
2380
3174
3967
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
208
416
624
832
1040
<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:
0.0848
Hom.:
148
Bravo
AF:
0.139
Asia WGS
AF:
0.162
AC:
566
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
7.5
DANN
Benign
0.60
PhyloP100
0.37
PromoterAI
0.0040
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs4726556; hg19: chr7-142374083; API