dbSNP rs8647: ATF5:c.*631G>A (chr19-49933723-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001193646.2(ATF5):c.*631G>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 0.303 in 153,028 control chromosomes in the GnomAD database, including 7,660 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 ( 7551 hom., cov: 30)

Exomes 𝑓: 0.41 ( 109 hom. )

Consequence

ATF5
NM_001193646.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

14 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001193646.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATF5	NM_001193646.2	MANE Select	c.*631G>A	3_prime_UTR	Exon 3 of 3	NP_001180575.1
ATF5	NM_001290746.2		c.*631G>A	3_prime_UTR	Exon 3 of 3	NP_001277675.1
ATF5	NM_012068.6		c.*631G>A	3_prime_UTR	Exon 4 of 4	NP_036200.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF5	ENST00000423777.7	TSL:1 MANE Select	c.*631G>A		3_prime_UTR	Exon 3 of 3	ENSP00000396954.1
	ENSG00000269179	ENST00000451973.1	TSL:2	n.*77+18168C>T		intron	N/A	ENSP00000391489.1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45808

AN:

151710

Hom.:

7552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.315

GnomAD4 exome

AF:

0.414

AC:

497

AN:

1200

Hom.:

109

Cov.:

AF XY:

0.436

AC XY:

309

AN XY:

708

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.464

AC:

348

AN:

750

Middle Eastern (MID)

AF:

0.119

AC:

AN:

European-Non Finnish (NFE)

AF:

0.347

AC:

104

AN:

300

Other (OTH)

AF:

0.432

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.302

AC:

45835

AN:

151828

Hom.:

7551

Cov.:

AF XY:

0.305

AC XY:

22635

AN XY:

74164

show subpopulations

African (AFR)

AF:

0.172

AC:

7134

AN:

41420

American (AMR)

AF:

0.340

AC:

5180

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

912

AN:

3468

East Asian (EAS)

AF:

0.442

AC:

2279

AN:

5152

South Asian (SAS)

AF:

0.204

AC:

981

AN:

4810

European-Finnish (FIN)

AF:

0.458

AC:

4819

AN:

10520

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23639

AN:

67906

Other (OTH)

AF:

0.316

AC:

667

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1542

3085

4627

6170

7712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.324

Hom.:

10844

Bravo

AF:

0.291

Asia WGS

AF:

0.302

AC:

1050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.35

(source)

DANN

Benign

0.45

PhyloP100

-0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over