NM_001286581.2:c.*142C>G

Variant names:

• chr11-611919-C-G
• rs702966
• NM_001286581.2:c.*142C>G

Variant summary

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

The NM_001286581.2(PHRF1):​c.*142C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 992,038 control chromosomes in the GnomAD database, including 24,985 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 (9236 hom., cov: 32)
  • Exomes 𝑓: 0.13 (15749 hom.)
• Consequence: PHRF1 NM_001286581.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 32 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286581.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHRF1	NM_001286581.2	MANE Select	c.*142C>G		3_prime_UTR	Exon 18 of 18	NP_001273510.1	Q9P1Y6-1
	PHRF1	NM_020901.4		c.*142C>G		3_prime_UTR	Exon 18 of 18	NP_065952.2	Q9P1Y6-3
	PHRF1	NM_001286582.2		c.*142C>G		3_prime_UTR	Exon 18 of 18	NP_001273511.1	F8WEF5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHRF1	ENST00000264555.10	TSL:1 MANE Select	c.*142C>G		3_prime_UTR	Exon 18 of 18	ENSP00000264555.5	Q9P1Y6-1
	PHRF1	ENST00000416188.3	TSL:1	c.*142C>G		3_prime_UTR	Exon 18 of 18	ENSP00000410626.2	Q9P1Y6-3
	PHRF1	ENST00000413872.6	TSL:1	c.*142C>G		3_prime_UTR	Exon 18 of 18	ENSP00000388589.2	F8WEF5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 46860 AN: 147178 Hom.: 9220 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.325

GnomAD4 exome AF: 0.130 AC: 110154 AN: 844742 Hom.: 15749 Cov.: 15 AF XY: 0.134 AC XY: 56598 AN XY: 422118

African (AFR) AF: 0.406 AC: 6362 AN: 15670

American (AMR) AF: 0.277 AC: 5907 AN: 21344

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 4556 AN: 16036

East Asian (EAS) AF: 0.0198 AC: 682 AN: 34416

South Asian (SAS) AF: 0.110 AC: 6498 AN: 58974

European-Finnish (FIN) AF: 0.200 AC: 6030 AN: 30222

Middle Eastern (MID) AF: 0.217 AC: 599 AN: 2764

European-Non Finnish (NFE) AF: 0.116 AC: 72487 AN: 625994

Other (OTH) AF: 0.179 AC: 7033 AN: 39322

GnomAD4 genome AF: 0.318 AC: 46911 AN: 147296 Hom.: 9236 Cov.: 32 AF XY: 0.307 AC XY: 22021 AN XY: 71800

African (AFR) AF: 0.517 AC: 20647 AN: 39954

American (AMR) AF: 0.302 AC: 4507 AN: 14934

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1160 AN: 3388

East Asian (EAS) AF: 0.0232 AC: 119 AN: 5130

South Asian (SAS) AF: 0.119 AC: 558 AN: 4708

European-Finnish (FIN) AF: 0.172 AC: 1748 AN: 10184

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17236 AN: 65780

Other (OTH) AF: 0.324 AC: 662 AN: 2044

Alfa AF: 0.155 Hom.: 255

Bravo AF: 0.345

Asia WGS AF: 0.0890 AC: 296 AN: 3338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		1.2
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		4.0
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: rs702966; hg19: chr11-611919;