Variant rs11623705 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001202559.1(CHURC1-FNTB):c.327+12924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 156,886 control chromosomes in the GnomAD database, including 833 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 0.090 ( 799 hom., cov: 32)

Exomes 𝑓: 0.11 ( 34 hom. )

Consequence

CHURC1-FNTB
NM_001202559.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.724

Variant links:

Genes affected

CHURC1-FNTB (HGNC:):

CHURC1-FNTB links:

CHURC1 (HGNC:20099): (churchill domain containing 1) Predicted to enable zinc ion binding activity. Predicted to be involved in positive regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

CHURC1 links:

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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHURC1-FNTB	NM_001202559.1 linkuse as main transcript	c.327+12924G>T		intron_variant
CHURC1-FNTB	NM_001202558.2 linkuse as main transcript	c.6+14878G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHURC1	ENST00000551093.6 linkuse as main transcript	c.247-4295G>T		intron_variant		2
CHURC1	ENST00000551947.6 linkuse as main transcript	c.176-4295G>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0901

AC:

13701

AN:

152056

Hom.:

798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0228

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0869

Gnomad ASJ

AF:

0.0983

Gnomad EAS

AF:

0.0718

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.0755

GnomAD4 exome

AF:

0.108

AC:

508

AN:

4712

Hom.:

AF XY:

0.101

AC XY:

241

AN XY:

2388

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0802

Gnomad4 ASJ exome

AF:

0.0577

Gnomad4 EAS exome

AF:

0.116

Gnomad4 SAS exome

AF:

0.0368

Gnomad4 FIN exome

AF:

0.171

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.0901

AC:

13704

AN:

152174

Hom.:

799

Cov.:

AF XY:

0.0917

AC XY:

6823

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0227

Gnomad4 AMR

AF:

0.0871

Gnomad4 ASJ

AF:

0.0983

Gnomad4 EAS

AF:

0.0720

Gnomad4 SAS

AF:

0.0239

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.112

Hom.:

1363

Bravo

AF:

0.0825

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

4.6

Dann

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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