rs915087517

Variant names:

• chr11-591426-A-C
• NM_001286581.2:c.463A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-591426-A-C
• chr11-591426-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001286581.2(PHRF1):​c.463A>C​(p.Ile155Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000206 in 1,457,512 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: PHRF1 NM_001286581.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26336163).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHRF1	NM_001286581.2	c.463A>C	p.Ile155Leu	missense_variant	Exon 5 of 18	ENST00000264555.10	NP_001273510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHRF1	ENST00000264555.10	c.463A>C	p.Ile155Leu	missense_variant	Exon 5 of 18	1	NM_001286581.2	ENSP00000264555.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1457512 Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3 AN XY: 724984

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Uncertain	0.057	T
BayesDel_noAF	Benign	-0.16
CADD	Benign	16
DANN	Benign	0.93
DEOGEN2	Benign	0.084	T;.;T;.
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.67
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.81	T;T;T;T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.26	T;T;T;T
MetaSVM	Benign	-0.64	T
MutationAssessor	Benign	1.7	L;.;.;L
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-1.5	N;N;N;N
REVEL	Uncertain	0.29
Sift	Uncertain	0.011	D;D;D;D
Sift4G	Benign	0.083	T;T;T;T
Polyphen		0.46	P;P;P;P
Vest4		0.51
MutPred		0.45		Gain of catalytic residue at I155 (P = 0.0041);.;.;Gain of catalytic residue at I155 (P = 0.0041);
MVP		0.24
MPC		0.12
ClinPred		0.44	T
GERP RS		1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.12
gMVP		0.52

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-591426;