Genetic Variant ENST00000506866.7:c.*36C>A (chr4-139496317-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000506866.7(SETD7):c.*36C>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 0.855 in 692,882 control chromosomes in the GnomAD database, including 254,255 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 0.83 ( 52290 hom., cov: 31)

Exomes 𝑓: 0.86 ( 201965 hom. )

Consequence

SETD7
ENST00000506866.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

Publications

14 publications found

Variant links:

Genes affected

SETD7 (HGNC:30412): (SET domain containing 7, histone lysine methyltransferase) Enables histone-lysine N-methyltransferase activity and p53 binding activity. Involved in peptidyl-lysine dimethylation and peptidyl-lysine monomethylation. Acts upstream of or within cellular response to DNA damage stimulus and heterochromatin organization. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

SETD7 links:

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new If you want to explore the variant's impact on the transcript ENST00000506866.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506866.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SETD7	NM_001306199.2		c.*36C>A		3_prime_UTR	Exon 8 of 8	NP_001293128.1	D6RJA0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SETD7	ENST00000506866.7	TSL:1	c.*36C>A		3_prime_UTR	Exon 8 of 8	ENSP00000427300.1	D6RJA0
	SETD7	ENST00000515101.1	TSL:3	n.483C>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.826

AC:

125546

AN:

151988

Hom.:

52244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.914

Gnomad AMR

AF:

0.814

Gnomad ASJ

AF:

0.837

Gnomad EAS

AF:

0.982

Gnomad SAS

AF:

0.895

Gnomad FIN

AF:

0.909

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.860

Gnomad OTH

AF:

0.829

GnomAD2 exomes

AF:

0.848

AC:

103216

AN:

121694

AF XY:

0.854

show subpopulations

Gnomad AFR exome

AF:

0.727

Gnomad AMR exome

AF:

0.757

Gnomad ASJ exome

AF:

0.833

Gnomad EAS exome

AF:

0.986

Gnomad FIN exome

AF:

0.897

Gnomad NFE exome

AF:

0.858

Gnomad OTH exome

AF:

0.867

GnomAD4 exome

AF:

0.863

AC:

466458

AN:

540776

Hom.:

201965

Cov.:

AF XY:

0.865

AC XY:

253023

AN XY:

292462

show subpopulations

African (AFR)

AF:

0.727

AC:

11133

AN:

15306

American (AMR)

AF:

0.763

AC:

25404

AN:

33300

Ashkenazi Jewish (ASJ)

AF:

0.833

AC:

16323

AN:

19594

East Asian (EAS)

AF:

0.978

AC:

31184

AN:

31888

South Asian (SAS)

AF:

0.887

AC:

54132

AN:

60994

European-Finnish (FIN)

AF:

0.898

AC:

29619

AN:

32992

Middle Eastern (MID)

AF:

0.921

AC:

3703

AN:

4022

European-Non Finnish (NFE)

AF:

0.861

AC:

269065

AN:

312498

Other (OTH)

AF:

0.858

AC:

25895

AN:

30182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

3035

6071

9106

12142

15177

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1016

2032

3048

4064

5080

<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:

0.826

AC:

125649

AN:

152106

Hom.:

52290

Cov.:

AF XY:

0.834

AC XY:

62002

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.723

AC:

29976

AN:

41452

American (AMR)

AF:

0.814

AC:

12446

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.837

AC:

2906

AN:

3470

East Asian (EAS)

AF:

0.982

AC:

5077

AN:

5172

South Asian (SAS)

AF:

0.895

AC:

4311

AN:

4816

European-Finnish (FIN)

AF:

0.909

AC:

9631

AN:

10598

Middle Eastern (MID)

AF:

0.908

AC:

267

AN:

294

European-Non Finnish (NFE)

AF:

0.860

AC:

58447

AN:

67996

Other (OTH)

AF:

0.831

AC:

1754

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1089

2178

3266

4355

5444

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

882

1764

2646

3528

4410

<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:

0.848

Hom.:

90697

Bravo

AF:

0.812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.88

(source)

DANN

Benign

0.45

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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