GeneBe

chr6-146749369-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024694.4(ADGB):​c.3366-3161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,110 control chromosomes in the GnomAD database, including 2,526 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 0.17 ( 2526 hom., cov: 32)

Consequence

ADGB
NM_024694.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Publications

0 publications found
Variant links:
Genes affected
ADGB (HGNC:21212): (androglobin) Predicted to enable calcium-dependent cysteine-type endopeptidase activity; heme binding activity; and oxygen binding activity. Predicted to be involved in proteolysis. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADGBNM_024694.4 linkc.3366-3161A>G intron_variant Intron 26 of 35 ENST00000397944.8 NP_078970.3 Q8N7X0-1Q9H5S1
LOC105378040XR_943093.2 linkn.60-12345T>C intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADGBENST00000397944.8 linkc.3366-3161A>G intron_variant Intron 26 of 35 5 NM_024694.4 ENSP00000381036.3 Q8N7X0-1

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26540
AN:
151992
Hom.:
2522
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.146
Gnomad AMR
AF:
0.125
Gnomad ASJ
AF:
0.166
Gnomad EAS
AF:
0.389
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.116
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.175
Gnomad OTH
AF:
0.182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.175
AC:
26561
AN:
152110
Hom.:
2526
Cov.:
32
AF XY:
0.172
AC XY:
12781
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.176
AC:
7285
AN:
41490
American (AMR)
AF:
0.125
AC:
1907
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.166
AC:
576
AN:
3470
East Asian (EAS)
AF:
0.389
AC:
2002
AN:
5146
South Asian (SAS)
AF:
0.228
AC:
1103
AN:
4830
European-Finnish (FIN)
AF:
0.116
AC:
1226
AN:
10596
Middle Eastern (MID)
AF:
0.136
AC:
40
AN:
294
European-Non Finnish (NFE)
AF:
0.175
AC:
11905
AN:
67992
Other (OTH)
AF:
0.182
AC:
384
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1110
2221
3331
4442
5552
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
296
592
888
1184
1480
<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:
0.171
Hom.:
540
Bravo
AF:
0.175
Asia WGS
AF:
0.258
AC:
899
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
2.3
DANN
Benign
0.71
PhyloP100
0.18
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs9403813; hg19: chr6-147070505; COSMIC: COSV62228442; API