GeneBe

16-30907166-C-G

Position:

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 0.322 in 151,868 control chromosomes in the GnomAD database, including 10,428 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 0.32 ( 10428 hom., cov: 31)

Consequence

CTF2P
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CTF2P use as main transcriptn.30907166C>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CTF2PENST00000412003.1 linkuse as main transcriptn.153+318G>C intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48838
AN:
151750
Hom.:
10426
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0764
Gnomad AMI
AF:
0.439
Gnomad AMR
AF:
0.392
Gnomad ASJ
AF:
0.525
Gnomad EAS
AF:
0.904
Gnomad SAS
AF:
0.196
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.390
Gnomad OTH
AF:
0.391
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48842
AN:
151868
Hom.:
10428
Cov.:
31
AF XY:
0.324
AC XY:
24044
AN XY:
74202
show subpopulations
Gnomad4 AFR
AF:
0.0762
Gnomad4 AMR
AF:
0.392
Gnomad4 ASJ
AF:
0.525
Gnomad4 EAS
AF:
0.904
Gnomad4 SAS
AF:
0.196
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.390
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.383
Hom.:
6965
Bravo
AF:
0.321
Asia WGS
AF:
0.471
AC:
1640
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
4.5
DANN
Benign
0.72

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: rs11649653; hg19: chr16-30918487; API