14-60503286-G-C

Position:

• chr14-60503286-G-C

Variant summary

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

The XM_017021250.3(C14orf39):​c.-3995C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,016 control chromosomes in the GnomAD database, including 53,550 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 0.83 (53550 hom., cov: 30)
• Consequence: C14orf39 XM_017021250.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

C14orf39 (HGNC:19849): (chromosome 14 open reading frame 39) Predicted to be involved in gamete generation and meiosis I. Predicted to be located in chromosome. Predicted to be active in central element. Implicated in primary ovarian insufficiency 18 and spermatogenic failure 52. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C14orf39	XM_017021250.3	c.-3995C>G		5_prime_UTR_variant	1/14		XP_016876739.1
C14orf39	XM_047431324.1	c.-143-3856C>G		intron_variant			XP_047287280.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C14orf39	ENST00000556799.1	c.-143-3856C>G		intron_variant		4		ENSP00000451441

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125747 AN: 151898 Hom.: 53526 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.828 AC: 125823 AN: 152016 Hom.: 53550 Cov.: 30 AF XY: 0.830 AC XY: 61706 AN XY: 74318

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.837

Alfa AF: 0.870 Hom.: 3453

Bravo AF: 0.815

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7160405; hg19: chr14-60970004;