rs370049093

Variant summary

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

The NM_001419873.1(PHF11):​c.-518_-503delCGGGCGGGCGGGCGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 691,834 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000060 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

PHF11
NM_001419873.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.703
Variant links:
Genes affected
PHF11 (HGNC:17024): (PHD finger protein 11) This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHF11NM_001040443.3 linkc.94+21_94+36delCGGGCGGGCGGGCGGG intron_variant Intron 1 of 9 ENST00000378319.8 NP_001035533.1 Q9UIL8-1B4DDL5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHF11ENST00000378319.8 linkc.94+14_94+29delGGGCGGGCGGGCGGGC intron_variant Intron 1 of 9 1 NM_001040443.3 ENSP00000367570.3 Q9UIL8-1

Frequencies

GnomAD3 genomes
AF:
0.0000600
AC:
9
AN:
149918
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000196
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000483
GnomAD4 exome
AF:
0.0000351
AC:
19
AN:
541806
Hom.:
0
AF XY:
0.0000298
AC XY:
8
AN XY:
268154
show subpopulations
Gnomad4 AFR exome
AF:
0.000684
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000459
Gnomad4 SAS exome
AF:
0.0000447
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000191
Gnomad4 OTH exome
AF:
0.0000394
GnomAD4 genome
AF:
0.0000600
AC:
9
AN:
150028
Hom.:
0
Cov.:
0
AF XY:
0.0000820
AC XY:
6
AN XY:
73184
show subpopulations
Gnomad4 AFR
AF:
0.000195
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370049093; hg19: chr13-50070244; API