chr4-120897567-A-C

Position:

• chr4-120897567-A-C

Variant summary

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

The NM_018699.4(PRDM5):​c.177+9907T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,000 control chromosomes in the GnomAD database, including 5,682 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 0.25 (5682 hom., cov: 32)
• Consequence: PRDM5 NM_018699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

PRDM5 (HGNC:9349): (PR/SET domain 5) The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]

PRDM5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDM5	NM_018699.4	c.177+9907T>G		intron_variant		ENST00000264808.8	NP_061169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDM5	ENST00000264808.8	c.177+9907T>G		intron_variant		1	NM_018699.4	ENSP00000264808.3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38656 AN: 151882 Hom.: 5670 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.260

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38708 AN: 152000 Hom.: 5682 Cov.: 32 AF XY: 0.252 AC XY: 18700 AN XY: 74288

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.258

Alfa AF: 0.213 Hom.: 1779

Bravo AF: 0.274

Asia WGS AF: 0.266 AC: 924 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.74

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: rs343166; hg19: chr4-121818722;