rs1064108

Positions:

• chr14-64933547-C-T

Variant summary

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

The NM_001386928.1(CHURC1):​c.*1317C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 976,432 control chromosomes in the GnomAD database, including 60,765 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 0.47 (20400 hom., cov: 32)
  • Exomes 𝑓: 0.30 (40365 hom.)
• Consequence: CHURC1 NM_001386928.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

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-FNTB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHURC1	NM_001386928.1	c.*1317C>T		3_prime_UTR_variant	4/4	ENST00000549115.7
CHURC1-FNTB	NM_001202559.1	c.327+7467C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHURC1	ENST00000549115.7	c.*1317C>T		3_prime_UTR_variant	4/4	1	NM_001386928.1	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70569 AN: 151866 Hom.: 20346 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.433

GnomAD4 exome AF: 0.300 AC: 247323 AN: 824448 Hom.: 40365 Cov.: 17 AF XY: 0.300 AC XY: 114139 AN XY: 381068

Gnomad4 AFR exome AF: 0.853

Gnomad4 AMR exome AF: 0.369

Gnomad4 ASJ exome AF: 0.390

Gnomad4 EAS exome AF: 0.704

Gnomad4 SAS exome AF: 0.367

Gnomad4 FIN exome AF: 0.351

Gnomad4 NFE exome AF: 0.283

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.465 AC: 70685 AN: 151984 Hom.: 20400 Cov.: 32 AF XY: 0.467 AC XY: 34662 AN XY: 74268

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.438

Alfa AF: 0.326 Hom.: 11963

Bravo AF: 0.488

Asia WGS AF: 0.560 AC: 1946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.53

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: rs1064108; hg19: chr14-65400265;