rs4902347

chr14-64944482-C-T

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+18402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.089 in 152,268 control chromosomes in the GnomAD database, including 789 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 0.089 (786 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3 hom.)
• Consequence: CHURC1-FNTB NM_001202559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHURC1-FNTB	NM_001202559.1	c.327+18402C>T		intron_variant
CHURC1-FNTB	NM_001202558.2	c.6+20356C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHURC1	ENST00000551947.6	c.*1161C>T		3_prime_UTR_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13543 AN: 152058 Hom.: 785 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0814

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0731

GnomAD4 exome AF: 0.120 AC: 11 AN: 92 Hom.: 3 Cov.: 0 AF XY: 0.115 AC XY: 9 AN XY: 78

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0890 AC: 13546 AN: 152176 Hom.: 786 Cov.: 32 AF XY: 0.0905 AC XY: 6729 AN XY: 74394

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.0815

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0706

Gnomad4 SAS AF: 0.0231

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.107 Hom.: 111

Bravo AF: 0.0810

Asia WGS AF: 0.0580 AC: 202 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	6.1
Dann	Benign	0.74

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: rs4902347; hg19: chr14-65411200;