rs3742599

Positions:

• chr14-64945190-C-A

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+19110C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,214 control chromosomes in the GnomAD database, including 1,775 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 0.15 (1775 hom., cov: 33)
• Consequence: CHURC1-FNTB NM_001202559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

CHURC1-FNTB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHURC1-FNTB	NM_001202559.1	c.327+19110C>A		intron_variant			NP_001189488.1
CHURC1-FNTB	NM_001202558.2	c.6+21064C>A		intron_variant			NP_001189487.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22106 AN: 152096 Hom.: 1773 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.145 AC: 22131 AN: 152214 Hom.: 1775 Cov.: 33 AF XY: 0.148 AC XY: 11007 AN XY: 74406

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.131

Alfa AF: 0.163 Hom.: 1421

Bravo AF: 0.138

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.037
DANN	Benign	0.78

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: rs3742599; hg19: chr14-65411908;