chr19-6543331-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 0.876 in 151,986 control chromosomes in the GnomAD database, including 58,411 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 0.88 ( 58411 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28
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=-1.03).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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:
0.876
AC:
133062
AN:
151870
Hom.:
58371
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.872
Gnomad AMI
AF:
0.971
Gnomad AMR
AF:
0.855
Gnomad ASJ
AF:
0.862
Gnomad EAS
AF:
0.805
Gnomad SAS
AF:
0.816
Gnomad FIN
AF:
0.860
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.896
Gnomad OTH
AF:
0.868
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.876
AC:
133158
AN:
151986
Hom.:
58411
Cov.:
30
AF XY:
0.872
AC XY:
64782
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.871
Gnomad4 AMR
AF:
0.856
Gnomad4 ASJ
AF:
0.862
Gnomad4 EAS
AF:
0.805
Gnomad4 SAS
AF:
0.816
Gnomad4 FIN
AF:
0.860
Gnomad4 NFE
AF:
0.896
Gnomad4 OTH
AF:
0.869
Alfa
AF:
0.888
Hom.:
81354
Bravo
AF:
0.877
Asia WGS
AF:
0.821
AC:
2854
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.61
DANN
Benign
0.31

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: rs348373; hg19: chr19-6543342; API