6-32445540-G-T

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 0.768 in 152,088 control chromosomes in the GnomAD database, including 45,037 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 0.77 ( 45037 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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:
0.768
AC:
116768
AN:
151970
Hom.:
45021
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.720
Gnomad AMI
AF:
0.895
Gnomad AMR
AF:
0.797
Gnomad ASJ
AF:
0.851
Gnomad EAS
AF:
0.833
Gnomad SAS
AF:
0.811
Gnomad FIN
AF:
0.723
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.784
Gnomad OTH
AF:
0.799
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.768
AC:
116836
AN:
152088
Hom.:
45037
Cov.:
31
AF XY:
0.767
AC XY:
57010
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.719
Gnomad4 AMR
AF:
0.796
Gnomad4 ASJ
AF:
0.851
Gnomad4 EAS
AF:
0.833
Gnomad4 SAS
AF:
0.811
Gnomad4 FIN
AF:
0.723
Gnomad4 NFE
AF:
0.784
Gnomad4 OTH
AF:
0.800
Alfa
AF:
0.791
Hom.:
50331
Bravo
AF:
0.774
Asia WGS
AF:
0.783
AC:
2725
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.6
DANN
Benign
0.44

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: rs2395182; hg19: chr6-32413317; API