6-137553271-A-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 0.428 in 152,072 control chromosomes in the GnomAD database, including 14,986 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 0.43 ( 14986 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.207
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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:
0.428
AC:
65110
AN:
151954
Hom.:
14977
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.259
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.461
Gnomad ASJ
AF:
0.371
Gnomad EAS
AF:
0.615
Gnomad SAS
AF:
0.559
Gnomad FIN
AF:
0.637
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.442
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.428
AC:
65153
AN:
152072
Hom.:
14986
Cov.:
32
AF XY:
0.438
AC XY:
32536
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.259
Gnomad4 AMR
AF:
0.461
Gnomad4 ASJ
AF:
0.371
Gnomad4 EAS
AF:
0.616
Gnomad4 SAS
AF:
0.558
Gnomad4 FIN
AF:
0.637
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.446
Alfa
AF:
0.460
Hom.:
26884
Bravo
AF:
0.408
Asia WGS
AF:
0.552
AC:
1919
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
5.8
DANN
Benign
0.78

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: rs9321619; hg19: chr6-137874408; API