GeneBe

rs8015211

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14
Variant links:
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]

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ACMG classification

Classification made for transcript

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 UniProt
ATG14NM_014924.5 linkuse as main transcriptc.1172+3090A>G intron_variant ENST00000247178.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATG14ENST00000247178.6 linkuse as main transcriptc.1172+3090A>G intron_variant 1 NM_014924.5 P1Q6ZNE5-1
ATG14ENST00000558189.1 linkuse as main transcriptn.1155+3090A>G intron_variant, non_coding_transcript_variant 2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8015211; hg19: chr14-55841447; API