chr14-55374729-T-C

Position:

• chr14-55374729-T-C

Variant summary

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

The NM_014924.5(ATG14):​c.1172+3090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,054 control chromosomes in the GnomAD database, including 7,067 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 0.30 (7067 hom., cov: 32)
• Consequence: ATG14 NM_014924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ATG14 (HGNC:19962): (autophagy related 14) Enables GTPase binding activity. Involved in several processes, including macroautophagy; regulation of phosphorylation; and response to mitochondrial depolarisation. Acts upstream of or within endosome to lysosome transport. Located in autophagosome and phagophore assembly site membrane. Is extrinsic component of omegasome membrane and extrinsic component of phagophore assembly site membrane. [provided by Alliance of Genome Resources, Apr 2022]

FBXO34 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG14	NM_014924.5	c.1172+3090A>G		intron_variant		ENST00000247178.6	NP_055739.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG14	ENST00000247178.6	c.1172+3090A>G		intron_variant		1	NM_014924.5	ENSP00000247178	P1
ATG14	ENST00000558189.1	n.1155+3090A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45051 AN: 151936 Hom.: 7062 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.296 AC: 45076 AN: 152054 Hom.: 7067 Cov.: 32 AF XY: 0.301 AC XY: 22392 AN XY: 74324

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.266

Alfa AF: 0.310 Hom.: 1343

Bravo AF: 0.274

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.26

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: rs8015211; hg19: chr14-55841447;