chr14-106686431-G-A

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 0.243 in 151,920 control chromosomes in the GnomAD database, including 4,984 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 0.24 ( 4984 hom., cov: 33)
Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.243
AC:
36952
AN:
151794
Hom.:
4981
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.243
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.346
Gnomad SAS
AF:
0.492
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.308
Gnomad NFE
AF:
0.260
Gnomad OTH
AF:
0.257
GnomAD4 exome
AF:
0.200
AC:
2
AN:
10
Hom.:
0
AF XY:
0.200
AC XY:
2
AN XY:
10
show subpopulations
Gnomad4 NFE exome
AF:
0.250
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.243
AC:
36973
AN:
151910
Hom.:
4984
Cov.:
33
AF XY:
0.248
AC XY:
18438
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.160
Gnomad4 AMR
AF:
0.244
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.491
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.260
Gnomad4 OTH
AF:
0.255
Alfa
AF:
0.247
Hom.:
1138
Bravo
AF:
0.235
Asia WGS
AF:
0.384
AC:
1337
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
3.5
DANN
Benign
0.44

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: rs8005468; hg19: chr14-107142448; API