Variant rs3826201 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDM7	NM_001098173.2 linkuse as main transcript	c.*381G>A		3_prime_UTR_variant	11/11	ENST00000449207.8	NP_001091643.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDM7	ENST00000449207.8 linkuse as main transcript	c.*381G>A		3_prime_UTR_variant	11/11	1	NM_001098173.2	ENSP00000396732	P1	Q9NQW5-3
PRDM7	ENST00000325921.10 linkuse as main transcript	n.1100G>A		non_coding_transcript_exon_variant	3/3	1

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

Gnomad4 AFR exome

AF:

0.0149

Gnomad4 AMR exome

AF:

0.298

Gnomad4 ASJ exome

AF:

0.0664

Gnomad4 EAS exome

AF:

0.643

Gnomad4 SAS exome

AF:

0.0953

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.0656

Gnomad4 OTH exome

AF:

0.105

GnomAD4 genome

AF:

0.0986

AC:

14973

AN:

151906

Hom.:

1862

Cov.:

AF XY:

0.111

AC XY:

8264

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.0186

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.0663

Gnomad4 EAS

AF:

0.599

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.0667

Gnomad4 OTH

AF:

0.0958

Alfa

AF:

0.0848

Hom.:

216

Bravo

AF:

0.0969

Asia WGS

AF:

0.276

AC:

961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.11

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over