6-76404370-G-A

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 0.459 in 151,890 control chromosomes in the GnomAD database, including 19,786 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 0.46 ( 19786 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240

Publications

2 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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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:
0.459
AC:
69672
AN:
151770
Hom.:
19778
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.115
Gnomad AMI
AF:
0.720
Gnomad AMR
AF:
0.512
Gnomad ASJ
AF:
0.690
Gnomad EAS
AF:
0.415
Gnomad SAS
AF:
0.551
Gnomad FIN
AF:
0.534
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.625
Gnomad OTH
AF:
0.494
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.459
AC:
69694
AN:
151890
Hom.:
19786
Cov.:
31
AF XY:
0.456
AC XY:
33869
AN XY:
74228
show subpopulations
African (AFR)
AF:
0.114
AC:
4735
AN:
41460
American (AMR)
AF:
0.512
AC:
7801
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
0.690
AC:
2391
AN:
3464
East Asian (EAS)
AF:
0.417
AC:
2146
AN:
5142
South Asian (SAS)
AF:
0.551
AC:
2655
AN:
4818
European-Finnish (FIN)
AF:
0.534
AC:
5637
AN:
10562
Middle Eastern (MID)
AF:
0.503
AC:
148
AN:
294
European-Non Finnish (NFE)
AF:
0.626
AC:
42471
AN:
67894
Other (OTH)
AF:
0.499
AC:
1053
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1554
3108
4662
6216
7770
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
630
1260
1890
2520
3150
<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:
0.507
Hom.:
2859
Bravo
AF:
0.446
Asia WGS
AF:
0.429
AC:
1495
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.2
DANN
Benign
0.50
PhyloP100
-0.024

Splicing

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

Publications

Other links and lift over

dbSNP: rs2451563; hg19: chr6-77114087; COSMIC: COSV69406001; API