rs3826201

Variant names:

• chr16-90057908-C-T
• rs3826201
• ENST00000325921.10:n.1100G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000325921.10(PRDM7):​n.1100G>A 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 0.0956 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 ENST00000325921.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.34
• Publications: 7 publications found

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]

ACMG classification

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: ENST00000325921.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14960 AN: 151790 Hom.: 1857 Cov.: 32

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.: 37 AF XY: 0.0943 AC XY: 66170 AN XY: 701730

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

GnomAD4 genome AF: 0.0986 AC: 14973 AN: 151906 Hom.: 1862 Cov.: 32 AF XY: 0.111 AC XY: 8264 AN XY: 74212

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: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0667 AC: 4530 AN: 67948

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

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
DANN	Benign	0.79
PhyloP100		-5.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3826201; hg19: chr16-90124316; COSMIC: COSV57987315; COSMIC: COSV57987315;