rs3759607

Variant names:

• chr14-23096934-A-G
• rs3759607
• NM_017924.4:c.-1-724A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017924.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C14orf119	NM_017924.4	MANE Select	c.-1-724A>G		intron	N/A	NP_060394.1	Q9NWQ9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C14orf119	ENST00000319074.6	TSL:1 MANE Select	c.-1-724A>G		intron	N/A	ENSP00000322238.4	Q9NWQ9
	C14orf119	ENST00000897765.1		c.-725A>G		5_prime_UTR_premature_start_codon_gain	Exon 2 of 2	ENSP00000567824.1
	C14orf119	ENST00000897765.1		c.-725A>G		5_prime_UTR	Exon 2 of 2	ENSP00000567824.1

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

African (AFR) AF: 0.157 AC: 6505 AN: 41516

American (AMR) AF: 0.0609 AC: 932 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1057 AN: 5176

South Asian (SAS) AF: 0.0530 AC: 256 AN: 4832

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4366 AN: 68032

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0742 Hom.: 628

Bravo AF: 0.0972

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.46
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3759607; hg19: chr14-23566143;