6-29964515-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 0.269 in 151,970 control chromosomes in the GnomAD database, including 5,776 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 0.27 ( 5776 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01
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=-0.62).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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:
0.270
AC:
40935
AN:
151856
Hom.:
5767
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.425
Gnomad AMR
AF:
0.250
Gnomad ASJ
AF:
0.258
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.328
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.269
AC:
40945
AN:
151970
Hom.:
5776
Cov.:
32
AF XY:
0.270
AC XY:
20085
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.214
Gnomad4 AMR
AF:
0.250
Gnomad4 ASJ
AF:
0.258
Gnomad4 EAS
AF:
0.245
Gnomad4 SAS
AF:
0.300
Gnomad4 FIN
AF:
0.328
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.265
Alfa
AF:
0.212
Hom.:
887
Bravo
AF:
0.259
Asia WGS
AF:
0.343
AC:
1184
AN:
3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
11
DANN
Benign
0.93

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: rs2523933; hg19: chr6-29932292; API