6-32670217-T-C

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 0.53 in 148,930 control chromosomes in the GnomAD database, including 21,861 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 0.53 ( 21861 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.751
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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:
0.530
AC:
78836
AN:
148816
Hom.:
21848
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.485
Gnomad AMI
AF:
0.558
Gnomad AMR
AF:
0.627
Gnomad ASJ
AF:
0.647
Gnomad EAS
AF:
0.811
Gnomad SAS
AF:
0.671
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.703
Gnomad NFE
AF:
0.508
Gnomad OTH
AF:
0.556
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.530
AC:
78882
AN:
148930
Hom.:
21861
Cov.:
30
AF XY:
0.531
AC XY:
38614
AN XY:
72672
show subpopulations
Gnomad4 AFR
AF:
0.485
Gnomad4 AMR
AF:
0.628
Gnomad4 ASJ
AF:
0.647
Gnomad4 EAS
AF:
0.811
Gnomad4 SAS
AF:
0.668
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.508
Gnomad4 OTH
AF:
0.561
Alfa
AF:
0.531
Hom.:
15943
Bravo
AF:
0.548
Asia WGS
AF:
0.728
AC:
2527
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.5
DANN
Benign
0.40

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: rs9274741; hg19: chr6-32637994; API