chr16-90057908-C-T

Position:

• chr16-90057908-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.34

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

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	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	c.*381G>A		3_prime_UTR_variant	11/11	1	NM_001098173.2	ENSP00000396732	P1
PRDM7	ENST00000325921.10	n.1100G>A		non_coding_transcript_exon_variant	3/3	1

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

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.: 32 AF XY: 0.111 AC XY: 8264 AN XY: 74212

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

Other links and lift over

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