GeneBe

chr6-137219796-GAA-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.00478 in 967,358 control chromosomes in the GnomAD database, including 121 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.019 ( 77 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 44 hom. )

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339

Publications

4 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0608 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:
0.0189
AC:
2881
AN:
152122
Hom.:
77
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0629
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0116
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000573
Gnomad OTH
AF:
0.0263
GnomAD4 exome
AF:
0.00213
AC:
1739
AN:
815118
Hom.:
44
AF XY:
0.00201
AC XY:
757
AN XY:
377042
show subpopulations
African (AFR)
AF:
0.0692
AC:
1068
AN:
15436
American (AMR)
AF:
0.00826
AC:
8
AN:
968
Ashkenazi Jewish (ASJ)
AF:
0.000993
AC:
5
AN:
5036
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3534
South Asian (SAS)
AF:
0.0000621
AC:
1
AN:
16110
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
256
Middle Eastern (MID)
AF:
0.00567
AC:
9
AN:
1586
European-Non Finnish (NFE)
AF:
0.000750
AC:
559
AN:
745568
Other (OTH)
AF:
0.00334
AC:
89
AN:
26624
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
74
148
222
296
370
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
72
144
216
288
360
<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:
0.0190
AC:
2886
AN:
152240
Hom.:
77
Cov.:
32
AF XY:
0.0183
AC XY:
1360
AN XY:
74450
show subpopulations
African (AFR)
AF:
0.0628
AC:
2607
AN:
41514
American (AMR)
AF:
0.0116
AC:
177
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.00115
AC:
4
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5180
South Asian (SAS)
AF:
0.000414
AC:
2
AN:
4826
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10604
Middle Eastern (MID)
AF:
0.00680
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
0.000573
AC:
39
AN:
68024
Other (OTH)
AF:
0.0260
AC:
55
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
148
296
443
591
739
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
28
56
84
112
140
<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:
0.0135
Hom.:
5
Bravo
AF:
0.0221
Asia WGS
AF:
0.00462
AC:
16
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs41401746; hg19: chr6-137540933; API