rs1055382

Positions:

• chr11-612182-T-C

Variant summary

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

The NM_001286581.2(PHRF1):​c.*405T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 306,236 control chromosomes in the GnomAD database, including 15,057 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 0.32 (9411 hom., cov: 34)
  • Exomes 𝑓: 0.25 (5646 hom.)
• Consequence: PHRF1 NM_001286581.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

PHRF1 (HGNC:24351): (PHD and ring finger domains 1) Predicted to enable RNA polymerase binding activity. Predicted to be involved in mRNA processing and transcription by RNA polymerase II. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHRF1	NM_001286581.2	c.*405T>C		3_prime_UTR_variant	18/18	ENST00000264555.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHRF1	ENST00000264555.10	c.*405T>C		3_prime_UTR_variant	18/18	1	NM_001286581.2	P5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49419 AN: 152118 Hom.: 9395 Cov.: 34

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.331

GnomAD4 exome AF: 0.247 AC: 38090 AN: 154000 Hom.: 5646 Cov.: 0 AF XY: 0.242 AC XY: 19118 AN XY: 79072

Gnomad4 AFR exome AF: 0.513

Gnomad4 AMR exome AF: 0.315

Gnomad4 ASJ exome AF: 0.326

Gnomad4 EAS exome AF: 0.0226

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.206

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.272

GnomAD4 genome AF: 0.325 AC: 49470 AN: 152236 Hom.: 9411 Cov.: 34 AF XY: 0.314 AC XY: 23377 AN XY: 74440

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.330

Alfa AF: 0.308 Hom.: 3144

Bravo AF: 0.345

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.38
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1055382; hg19: chr11-612182;