dbSNP rs3826201: PRDM7:c.*381G>A (chr16-90057908-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001098173.2(PRDM7):c.*381G>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 0.0956 in 1,564,844 control chromosomes in the GnomAD database, including 16,184 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 0.099 ( 1862 hom., cov: 32)

Exomes 𝑓: 0.095 ( 14322 hom. )

Consequence

PRDM7
NM_001098173.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.34

Publications

7 publications found

Variant links:

Genes affected

PRDM7 (HGNC:9351): (PR/SET domain 7) This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]

PRDM7 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098173.2. 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
	PRDM7	NM_001098173.2	MANE Select	c.*381G>A		3_prime_UTR	Exon 11 of 11	NP_001091643.1	Q9NQW5-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM7	ENST00000449207.8	TSL:1 MANE Select	c.*381G>A		3_prime_UTR	Exon 11 of 11	ENSP00000396732.2	Q9NQW5-3
	PRDM7	ENST00000325921.10	TSL:1	n.1100G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0986

AC:

14960

AN:

151790

Hom.:

1857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0187

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.0663

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.0414

Gnomad NFE

AF:

0.0667

Gnomad OTH

AF:

0.0988

GnomAD4 exome

AF:

0.0953

AC:

134630

AN:

1412938

Hom.:

14322

Cov.:

AF XY:

0.0943

AC XY:

66170

AN XY:

701730

show subpopulations

African (AFR)

AF:

0.0149

AC:

483

AN:

32522

American (AMR)

AF:

0.298

AC:

12814

AN:

42974

Ashkenazi Jewish (ASJ)

AF:

0.0664

AC:

1634

AN:

24608

East Asian (EAS)

AF:

0.643

AC:

23190

AN:

36070

South Asian (SAS)

AF:

0.0953

AC:

8167

AN:

85726

European-Finnish (FIN)

AF:

0.231

AC:

11123

AN:

48224

Middle Eastern (MID)

AF:

0.0614

AC:

340

AN:

5538

European-Non Finnish (NFE)

AF:

0.0656

AC:

70836

AN:

1079968

Other (OTH)

AF:

0.105

AC:

6043

AN:

57308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

5750

11501

17251

23002

28752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3052

6104

9156

12208

15260

<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:

0.0986

AC:

14973

AN:

151906

Hom.:

1862

Cov.:

AF XY:

0.111

AC XY:

8264

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.0186

AC:

772

AN:

41438

American (AMR)

AF:

0.202

AC:

3083

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0663

AC:

230

AN:

3470

East Asian (EAS)

AF:

0.599

AC:

3089

AN:

5158

South Asian (SAS)

AF:

0.110

AC:

528

AN:

4794

European-Finnish (FIN)

AF:

0.239

AC:

2515

AN:

10516

Middle Eastern (MID)

AF:

0.0445

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0667

AC:

4530

AN:

67948

Other (OTH)

AF:

0.0958

AC:

202

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

591

1182

1774

2365

2956

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0911

Hom.:

810

Bravo

AF:

0.0969

Asia WGS

AF:

0.276

AC:

961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.11

(source)

DANN

Benign

0.79

PhyloP100

-5.3

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