19-6941150-G-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 0.696 in 151,884 control chromosomes in the GnomAD database, including 37,062 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 0.70 ( 37062 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.482
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=-1.02).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.696
AC:
105693
AN:
151766
Hom.:
37043
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.617
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.704
Gnomad ASJ
AF:
0.706
Gnomad EAS
AF:
0.687
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.726
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.685
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.696
AC:
105752
AN:
151884
Hom.:
37062
Cov.:
30
AF XY:
0.696
AC XY:
51669
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.617
Gnomad4 AMR
AF:
0.704
Gnomad4 ASJ
AF:
0.706
Gnomad4 EAS
AF:
0.686
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.726
Gnomad4 NFE
AF:
0.738
Gnomad4 OTH
AF:
0.677
Alfa
AF:
0.623
Hom.:
1804
Bravo
AF:
0.693
Asia WGS
AF:
0.617
AC:
2148
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
6.6
DANN
Benign
0.35

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: rs460375; hg19: chr19-6941161; API