Variant rs8667 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001193646.2(ATF5):c.*22G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,547,772 control chromosomes in the GnomAD database, including 87,077 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 ( 7618 hom., cov: 30)

Exomes 𝑓: 0.33 ( 79459 hom. )

Consequence

ATF5
NM_001193646.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.392

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:

MIR4751 (HGNC:41819): (microRNA 4751) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR4751 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATF5	NM_001193646.2 linkuse as main transcript	c.*22G>A		3_prime_UTR_variant	3/3	ENST00000423777.7
MIR4751	NR_039906.1 linkuse as main transcript	n.51G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
ATF5	ENST00000423777.7 linkuse as main transcript	c.*22G>A	3_prime_UTR_variant	3/3	1	NM_001193646.2	P1
MIR4751	ENST00000578027.1 linkuse as main transcript	n.51G>A	non_coding_transcript_exon_variant	1/1
ATF5	ENST00000595125.5 linkuse as main transcript	c.*22G>A	3_prime_UTR_variant	4/4	2		P1

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

46063

AN:

151776

Hom.:

7619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.226

Gnomad NFE

AF:

0.349

Gnomad OTH

AF:

0.317

GnomAD3 exomes

AF:

0.340

AC:

66916

AN:

196838

Hom.:

11963

AF XY:

0.335

AC XY:

35400

AN XY:

105578

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.373

Gnomad ASJ exome

AF:

0.287

Gnomad EAS exome

AF:

0.447

Gnomad SAS exome

AF:

0.208

Gnomad FIN exome

AF:

0.462

Gnomad NFE exome

AF:

0.345

Gnomad OTH exome

AF:

0.331

GnomAD4 exome

AF:

0.332

AC:

464104

AN:

1395878

Hom.:

79459

Cov.:

AF XY:

0.329

AC XY:

225463

AN XY:

685780

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.366

Gnomad4 ASJ exome

AF:

0.287

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.200

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.338

Gnomad4 OTH exome

AF:

0.312

GnomAD4 genome

AF:

0.303

AC:

46091

AN:

151894

Hom.:

7618

Cov.:

AF XY:

0.307

AC XY:

22754

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.349

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.327

Hom.:

3834

Bravo

AF:

0.293

Asia WGS

AF:

0.304

AC:

1058

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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