Variant 19-49932741-C-T 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.498C>T(p.Cys166Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0789 in 1,608,706 control chromosomes in the GnomAD database, including 5,361 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 0.079 ( 510 hom., cov: 26)

Exomes 𝑓: 0.079 ( 4851 hom. )

Consequence

ATF5
NM_001193646.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.655

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:

ENSG00000269179 (HGNC:):

ENSG00000269179 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=0.655 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATF5	NM_001193646.2 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	3/3	ENST00000423777.7	NP_001180575.1	Q9Y2D1A0A024QZG3
ATF5	NM_001290746.2 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	3/3		NP_001277675.1	Q9Y2D1A0A024QZG3
ATF5	NM_012068.6 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	4/4		NP_036200.2	Q9Y2D1A0A024QZG3
ATF5	XM_011526629.4 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	3/3		XP_011524931.1	Q9Y2D1A0A024QZG3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ATF5	ENST00000423777.7 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	3/3	1	NM_001193646.2	ENSP00000396954.1	Q9Y2D1
ENSG00000269179	ENST00000451973.1 linkuse as main transcript	n.*77+19150G>A		intron_variant		2		ENSP00000391489.1	H7BZU6
ATF5	ENST00000595125.5 linkuse as main transcript	c.498C>T	p.Cys166Cys	synonymous_variant	4/4	2		ENSP00000470633.1	Q9Y2D1

Frequencies

GnomAD3 genomes

AF:

0.0792

AC:

11834

AN:

149394

Hom.:

510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0793

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.0643

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.0869

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0732

Gnomad OTH

AF:

0.0775

GnomAD3 exomes

AF:

0.0834

AC:

20320

AN:

243500

Hom.:

899

AF XY:

0.0864

AC XY:

11422

AN XY:

132142

show subpopulations

Gnomad AFR exome

AF:

0.0782

Gnomad AMR exome

AF:

0.0681

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.0835

Gnomad SAS exome

AF:

0.123

Gnomad FIN exome

AF:

0.0991

Gnomad NFE exome

AF:

0.0738

Gnomad OTH exome

AF:

0.0811

GnomAD4 exome

AF:

0.0788

AC:

115022

AN:

1459200

Hom.:

4851

Cov.:

AF XY:

0.0805

AC XY:

58404

AN XY:

725638

show subpopulations

Gnomad4 AFR exome

AF:

0.0812

Gnomad4 AMR exome

AF:

0.0702

Gnomad4 ASJ exome

AF:

0.0994

Gnomad4 EAS exome

AF:

0.0843

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.0946

Gnomad4 NFE exome

AF:

0.0737

Gnomad4 OTH exome

AF:

0.0827

GnomAD4 genome

AF:

0.0791

AC:

11829

AN:

149506

Hom.:

510

Cov.:

AF XY:

0.0822

AC XY:

5989

AN XY:

72874

show subpopulations

Gnomad4 AFR

AF:

0.0792

Gnomad4 AMR

AF:

0.0642

Gnomad4 ASJ

AF:

0.0942

Gnomad4 EAS

AF:

0.0869

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.0732

Gnomad4 OTH

AF:

0.0762

Alfa

AF:

0.0777

Hom.:

260

Bravo

AF:

0.0787

Asia WGS

AF:

0.110

AC:

380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.7

DANN

Benign

0.75

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.3

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