Variant 12-2792404-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000540428.1(CBX3P4):n.299+1593A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,936 control chromosomes in the GnomAD database, including 1,745 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 0.14 ( 1745 hom., cov: 31)

Consequence

CBX3P4
ENST00000540428.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403

Variant links:

Genes affected

ITFG2-AS1 (HGNC:):

ITFG2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITFG2-AS1	NR_146317.1 linkuse as main transcript	n.433+4473A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ITFG2-AS1	ENST00000540093.2 linkuse as main transcript	n.411+4473A>G	intron_variant	3
CBX3P4	ENST00000540428.1 linkuse as main transcript	n.299+1593A>G	intron_variant	2
ITFG2-AS1	ENST00000636122.1 linkuse as main transcript	n.46+2571A>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21640

AN:

151816

Hom.:

1752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.142

AC:

21634

AN:

151936

Hom.:

1745

Cov.:

AF XY:

0.148

AC XY:

10985

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.128

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.139

Hom.:

1189

Bravo

AF:

0.138

Asia WGS

AF:

0.259

AC:

901

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.8

DANN

Benign

0.63

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over