19-2714172-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 0.014 ( 76 hom., cov: 9)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 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:
0.0143
AC:
880
AN:
61602
Hom.:
76
Cov.:
9
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00972
Gnomad ASJ
AF:
0.000480
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000716
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00833
Gnomad NFE
AF:
0.000635
Gnomad OTH
AF:
0.0113
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0143
AC:
883
AN:
61626
Hom.:
76
Cov.:
9
AF XY:
0.0146
AC XY:
424
AN XY:
28952
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.00970
Gnomad4 ASJ
AF:
0.000480
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000717
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000635
Gnomad4 OTH
AF:
0.0112
Alfa
AF:
0.0232
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.1
DANN
Benign
0.52

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: rs185543003; hg19: chr19-2714170; API