Genetic Variant PRDM15:n.*2286C>T (chr21-41800831-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 ENST00000441787.5(PRDM15):n.*2286C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 165,690 control chromosomes in the GnomAD database, including 10,436 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 0.35 ( 9821 hom., cov: 33)

Exomes 𝑓: 0.29 ( 615 hom. )

Consequence

PRDM15
ENST00000441787.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.519

Publications

5 publications found

Variant links:

Genes affected

PRDM15 (HGNC:13999): (PR/SET domain 15) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

PRDM15 links:

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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 (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDM15	NM_001040424.3 link	c.*409C>T		3_prime_UTR_variant	Exon 24 of 24	ENST00000398548.6	NP_001035514.2	P57071

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM15	ENST00000398548.6 link	c.*409C>T		3_prime_UTR_variant	Exon 24 of 24	1	NM_001040424.3	ENSP00000381556.2		P57071

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53074

AN:

152008

Hom.:

9803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.291

AC:

3943

AN:

13564

Hom.:

615

Cov.:

AF XY:

0.291

AC XY:

1963

AN XY:

6756

show subpopulations

African (AFR)

AF:

0.438

AC:

247

AN:

564

American (AMR)

AF:

0.244

AC:

144

AN:

590

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

117

AN:

490

East Asian (EAS)

AF:

0.267

AC:

142

AN:

532

South Asian (SAS)

AF:

0.314

AC:

AN:

210

European-Finnish (FIN)

AF:

0.254

AC:

142

AN:

560

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.289

AC:

2801

AN:

9684

Other (OTH)

AF:

0.302

AC:

260

AN:

862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

136

272

409

545

681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<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:

0.349

AC:

53131

AN:

152126

Hom.:

9821

Cov.:

AF XY:

0.346

AC XY:

25754

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.473

AC:

19604

AN:

41484

American (AMR)

AF:

0.293

AC:

4476

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

916

AN:

3470

East Asian (EAS)

AF:

0.291

AC:

1505

AN:

5178

South Asian (SAS)

AF:

0.390

AC:

1877

AN:

4818

European-Finnish (FIN)

AF:

0.272

AC:

2873

AN:

10574

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20835

AN:

67984

Other (OTH)

AF:

0.334

AC:

705

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1774

3547

5321

7094

8868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.318

Hom.:

13299

Bravo

AF:

0.357

Asia WGS

AF:

0.307

AC:

1070

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.2

(source)

DANN

Benign

0.29

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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