Genetic Variant ENST00000481439.1:n.22delA (chr13-49444704-CA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000481439.1(SETDB2):n.22delA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 16037 hom., cov: 0)

Exomes 𝑓: 0.46 ( 119 hom. )

Consequence

SETDB2
ENST00000481439.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.68

Publications

2 publications found

Variant links:

Genes affected

SETDB2 (HGNC:20263): (SET domain bifurcated histone lysine methyltransferase 2) This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occurs from this gene to the downstream PHF11 (PHD finger protein 11) gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

SETDB2 links:

SETDB2-PHF11 (HGNC:):

SETDB2-PHF11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SETDB2	NM_001160308.3 link	c.-494delA		5_prime_UTR_variant	Exon 1 of 14	ENST00000611815.2	NP_001153780.1	Q96T68-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SETDB2	ENST00000481439.1 link	n.22delA	non_coding_transcript_exon_variant	Exon 1 of 2	1
SETDB2	ENST00000611815.2 link	c.-494delA	5_prime_UTR_variant	Exon 1 of 14	5	NM_001160308.3	ENSP00000482240.2	Q96T68-2A0A087WYZ9
SETDB2	ENST00000354234.8 link	c.-494delA	5_prime_UTR_variant	Exon 1 of 15	1		ENSP00000346175.5	Q96T68-1

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65771

AN:

151644

Hom.:

16032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.516

Gnomad EAS

AF:

0.502

Gnomad SAS

AF:

0.361

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.470

GnomAD4 exome

AF:

0.460

AC:

440

AN:

956

Hom.:

119

Cov.:

AF XY:

0.425

AC XY:

226

AN XY:

532

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.360

AC:

AN:

150

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.294

AC:

AN:

126

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.511

AC:

325

AN:

636

Other (OTH)

AF:

0.625

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

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:

0.433

AC:

65781

AN:

151762

Hom.:

16037

Cov.:

AF XY:

0.433

AC XY:

32077

AN XY:

74160

show subpopulations

African (AFR)

AF:

0.194

AC:

8035

AN:

41514

American (AMR)

AF:

0.470

AC:

7170

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.516

AC:

1789

AN:

3464

East Asian (EAS)

AF:

0.502

AC:

2576

AN:

5136

South Asian (SAS)

AF:

0.361

AC:

1738

AN:

4820

European-Finnish (FIN)

AF:

0.532

AC:

5578

AN:

10480

Middle Eastern (MID)

AF:

0.541

AC:

158

AN:

292

European-Non Finnish (NFE)

AF:

0.551

AC:

37329

AN:

67786

Other (OTH)

AF:

0.470

AC:

989

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1797

3594

5390

7187

8984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.172

Hom.:

707

Bravo

AF:

0.424

Asia WGS

AF:

0.421

AC:

1462

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.7

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over