Variant rs283525 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001193646.2(ATF5):c.247T>C(p.Leu83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,591,096 control chromosomes in the GnomAD database, including 288,886 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 0.63 ( 27666 hom., cov: 18)

Exomes 𝑓: 0.60 ( 261220 hom. )

Consequence

ATF5
NM_001193646.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Variant links:

Genes affected

ATF5 (HGNC:790): (activating transcription factor 5) Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and tubulin binding activity. Involved in several processes, including fat cell differentiation; regulation of cell cycle process; and regulation of transcription, DNA-templated. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ATF5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=0.083 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ATF5	NM_001193646.2 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	3/3	ENST00000423777.7
ATF5	NM_001290746.2 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	3/3
ATF5	NM_012068.6 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	4/4
ATF5	XM_011526629.4 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
ATF5	ENST00000423777.7 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	3/3	1	NM_001193646.2	P1
ATF5	ENST00000595125.5 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	4/4	2		P1
ATF5	ENST00000596658.1 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	3/3	2
ATF5	ENST00000597227.5 linkuse as main transcript	c.247T>C	p.Leu83=	synonymous_variant	4/4	3

Frequencies

GnomAD3 genomes

AF:

0.627

AC:

86725

AN:

138208

Hom.:

27626

Cov.:

show subpopulations

Gnomad AFR

AF:

0.715

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.698

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.650

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.613

GnomAD3 exomes

AF:

0.621

AC:

154285

AN:

248504

Hom.:

48433

AF XY:

0.616

AC XY:

83055

AN XY:

134824

show subpopulations

Gnomad AFR exome

AF:

0.725

Gnomad AMR exome

AF:

0.651

Gnomad ASJ exome

AF:

0.535

Gnomad EAS exome

AF:

0.705

Gnomad SAS exome

AF:

0.604

Gnomad FIN exome

AF:

0.667

Gnomad NFE exome

AF:

0.588

Gnomad OTH exome

AF:

0.594

GnomAD4 exome

AF:

0.597

AC:

867199

AN:

1452776

Hom.:

261220

Cov.:

AF XY:

0.597

AC XY:

431442

AN XY:

723104

show subpopulations

Gnomad4 AFR exome

AF:

0.727

Gnomad4 AMR exome

AF:

0.650

Gnomad4 ASJ exome

AF:

0.538

Gnomad4 EAS exome

AF:

0.754

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.584

Gnomad4 OTH exome

AF:

0.593

GnomAD4 genome

AF:

0.628

AC:

86833

AN:

138320

Hom.:

27666

Cov.:

AF XY:

0.627

AC XY:

41742

AN XY:

66536

show subpopulations

Gnomad4 AFR

AF:

0.716

Gnomad4 AMR

AF:

0.594

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.698

Gnomad4 SAS

AF:

0.599

Gnomad4 FIN

AF:

0.650

Gnomad4 NFE

AF:

0.588

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.597

Hom.:

41033

Bravo

AF:

0.641

EpiCase

AF:

0.594

EpiControl

AF:

0.585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.9

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over