Genetic Variant ULK3:c.*1068A>G (chr15-74836160-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001099436.4(ULK3):c.*1068A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,118 control chromosomes in the GnomAD database, including 35,560 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 0.68 ( 35559 hom., cov: 33)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

ULK3
NM_001099436.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.958

Publications

27 publications found

Variant links:

Genes affected

ULK3 (HGNC:19703): (unc-51 like kinase 3) Enables protein serine/threonine kinase activity. Involved in several processes, including fibroblast activation; protein autophosphorylation; and regulation of smoothened signaling pathway. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ULK3 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099436.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ULK3	NM_001099436.4	MANE Select	c.*1068A>G	3_prime_UTR	Exon 16 of 16	NP_001092906.3	Q6PHR2-1
ULK3	NM_001411082.1		c.*1068A>G	3_prime_UTR	Exon 16 of 16	NP_001398011.1	Q6PHR2-4
ULK3	NM_001284364.3		c.*1068A>G	3_prime_UTR	Exon 16 of 16	NP_001271293.2	Q6PHR2-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ULK3	ENST00000440863.7	TSL:2 MANE Select	c.*1068A>G	3_prime_UTR	Exon 16 of 16	ENSP00000400312.2	Q6PHR2-1
ULK3	ENST00000569437.5	TSL:1	c.*1068A>G	3_prime_UTR	Exon 16 of 16	ENSP00000456051.1	Q6PHR2-3
ULK3	ENST00000566479.5	TSL:1	n.2673A>G	non_coding_transcript_exon	Exon 15 of 15

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103722

AN:

151994

Hom.:

35533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.627

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.684

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.673

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.671

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.682

AC:

103803

AN:

152112

Hom.:

35559

Cov.:

AF XY:

0.680

AC XY:

50533

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.627

AC:

25992

AN:

41474

American (AMR)

AF:

0.684

AC:

10465

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

2404

AN:

3470

East Asian (EAS)

AF:

0.724

AC:

3743

AN:

5168

South Asian (SAS)

AF:

0.672

AC:

3239

AN:

4822

European-Finnish (FIN)

AF:

0.685

AC:

7241

AN:

10576

Middle Eastern (MID)

AF:

0.738

AC:

217

AN:

294

European-Non Finnish (NFE)

AF:

0.712

AC:

48378

AN:

67994

Other (OTH)

AF:

0.673

AC:

1419

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1710

3420

5130

6840

8550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

824

1648

2472

3296

4120

<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:

0.703

Hom.:

128047

Bravo

AF:

0.683

Asia WGS

AF:

0.730

AC:

2538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.36

(source)

DANN

Benign

0.34

PhyloP100

-0.96

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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