6-19990741-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 0.671 in 151,828 control chromosomes in the GnomAD database, including 34,834 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 0.67 ( 34834 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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:
0.670
AC:
101708
AN:
151710
Hom.:
34784
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.802
Gnomad AMI
AF:
0.559
Gnomad AMR
AF:
0.669
Gnomad ASJ
AF:
0.559
Gnomad EAS
AF:
0.807
Gnomad SAS
AF:
0.613
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.634
Gnomad NFE
AF:
0.607
Gnomad OTH
AF:
0.633
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.671
AC:
101821
AN:
151828
Hom.:
34834
Cov.:
31
AF XY:
0.668
AC XY:
49511
AN XY:
74160
show subpopulations
Gnomad4 AFR
AF:
0.802
Gnomad4 AMR
AF:
0.669
Gnomad4 ASJ
AF:
0.559
Gnomad4 EAS
AF:
0.808
Gnomad4 SAS
AF:
0.613
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.607
Gnomad4 OTH
AF:
0.633
Alfa
AF:
0.617
Hom.:
50029
Bravo
AF:
0.686
Asia WGS
AF:
0.692
AC:
2388
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.22
DANN
Benign
0.21

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: rs965037; hg19: chr6-19990972; API