rs3759607

chr14-23096934-A-G

Variant summary

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

The NM_017924.4(C14orf119):c.-1-724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 152,256 control chromosomes in the GnomAD database, including 838 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 0.092 (838 hom., cov: 31)
• Consequence: C14orf119 NM_017924.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

Genes affected

C14orf119 (HGNC:20270): (chromosome 14 open reading frame 119) Located in cytosol and mitochondrion. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C14orf119	NM_017924.4	c.-1-724A>G		intron_variant		ENST00000319074.6
C14orf119	XM_017021390.3	c.-1-724A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C14orf119	ENST00000319074.6	c.-1-724A>G		intron_variant		1	NM_017924.4	P1
C14orf119	ENST00000554203.1	c.-17-708A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13995 AN: 152138 Hom.: 832 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0519

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0921 AC: 14024 AN: 152256 Hom.: 838 Cov.: 31 AF XY: 0.0917 AC XY: 6831 AN XY: 74460

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0609

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.0530

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0642

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0709 Hom.: 424

Bravo AF: 0.0972

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.0
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs3759607; hg19: chr14-23566143;