rs10133290

Positions:

• chr14-64937724-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001202559.1(CHURC1-FNTB):​c.327+11644A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,134 control chromosomes in the GnomAD database, including 6,106 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 0.26 (6106 hom., cov: 32)
• Consequence: CHURC1-FNTB NM_001202559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

CHURC1-FNTB (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHURC1-FNTB	NM_001202559.1	c.327+11644A>C		intron_variant			NP_001189488.1
CHURC1-FNTB	NM_001202558.2	c.6+13598A>C		intron_variant			NP_001189487.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHURC1	ENST00000551093.6	c.247-5575A>C		intron_variant		2		ENSP00000446610
CHURC1	ENST00000551947.6	c.176-5575A>C		intron_variant		2		ENSP00000446697

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40210 AN: 152016 Hom.: 6081 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.265 AC: 40298 AN: 152134 Hom.: 6106 Cov.: 32 AF XY: 0.266 AC XY: 19807 AN XY: 74378

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.241

Alfa AF: 0.230 Hom.: 1225

Bravo AF: 0.270

Asia WGS AF: 0.259 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.63

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

Other links and lift over

dbSNP: rs10133290; hg19: chr14-65404442;