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GeneBe

6-32730008-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.505 in 151,824 control chromosomes in the GnomAD database, including 20,498 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 0.51 ( 20498 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.176
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.505
AC:
76683
AN:
151706
Hom.:
20481
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.330
Gnomad AMI
AF:
0.731
Gnomad AMR
AF:
0.588
Gnomad ASJ
AF:
0.532
Gnomad EAS
AF:
0.711
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.581
Gnomad MID
AF:
0.586
Gnomad NFE
AF:
0.549
Gnomad OTH
AF:
0.535
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.505
AC:
76741
AN:
151824
Hom.:
20498
Cov.:
32
AF XY:
0.512
AC XY:
38006
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.330
Gnomad4 AMR
AF:
0.588
Gnomad4 ASJ
AF:
0.532
Gnomad4 EAS
AF:
0.711
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.581
Gnomad4 NFE
AF:
0.549
Gnomad4 OTH
AF:
0.542
Alfa
AF:
0.388
Hom.:
1111
Bravo
AF:
0.501
Asia WGS
AF:
0.669
AC:
2321
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
7.3
Dann
Benign
0.53

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2859113; hg19: chr6-32697785; COSMIC: COSV70889578; API