14-60490561-C-T

Position:

• chr14-60490561-C-T

Variant summary

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

The ENST00000556799.1(C14orf39):​c.-8-5475G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,894 control chromosomes in the GnomAD database, including 19,436 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 0.45 (19436 hom., cov: 31)
• Consequence: C14orf39 ENST00000556799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C14orf39	XM_047431324.1	c.-8-5475G>A		intron_variant			XP_047287280.1
C14orf39	XM_017021250.3	c.-5+8735G>A		intron_variant			XP_016876739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C14orf39	ENST00000556799.1	c.-8-5475G>A		intron_variant		4		ENSP00000451441.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68536 AN: 151778 Hom.: 19429 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.451 AC: 68561 AN: 151894 Hom.: 19436 Cov.: 31 AF XY: 0.457 AC XY: 33942 AN XY: 74236

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.426

Alfa AF: 0.529 Hom.: 2993

Bravo AF: 0.428

Asia WGS AF: 0.321 AC: 1117 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2093210; hg19: chr14-60957279;