14-88561547-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 0.569 in 151,942 control chromosomes in the GnomAD database, including 26,878 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 0.57 ( 26878 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98
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=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.688 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:
0.570
AC:
86486
AN:
151824
Hom.:
26884
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.594
Gnomad AMR
AF:
0.699
Gnomad ASJ
AF:
0.741
Gnomad EAS
AF:
0.568
Gnomad SAS
AF:
0.440
Gnomad FIN
AF:
0.730
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.672
Gnomad OTH
AF:
0.626
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.569
AC:
86503
AN:
151942
Hom.:
26878
Cov.:
31
AF XY:
0.575
AC XY:
42696
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.308
Gnomad4 AMR
AF:
0.699
Gnomad4 ASJ
AF:
0.741
Gnomad4 EAS
AF:
0.568
Gnomad4 SAS
AF:
0.439
Gnomad4 FIN
AF:
0.730
Gnomad4 NFE
AF:
0.672
Gnomad4 OTH
AF:
0.622
Alfa
AF:
0.499
Hom.:
1612
Bravo
AF:
0.562
Asia WGS
AF:
0.519
AC:
1807
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
1.8
DANN
Benign
0.71

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: rs11159859; hg19: chr14-89027891; API