chr13-49496108-GGGGCGGGCGGGCGGGC-G

Variant names:

• chr13-49496108-GGGGCGGGCGGGCGGGC-G
• rs370049093
• NM_001040443.3:c.94+21_94+36delCGGGCGGGCGGGCGGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001040443.3(PHF11):​c.94+21_94+36delCGGGCGGGCGGGCGGG variant causes a intron 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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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_001040443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 1 publications found

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]

SETDB2-PHF11 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3	c.94+21_94+36delCGGGCGGGCGGGCGGG		intron_variant	Intron 1 of 9	ENST00000378319.8	NP_001035533.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8	c.94+14_94+29delGGGCGGGCGGGCGGGC		intron_variant	Intron 1 of 9	1	NM_001040443.3	ENSP00000367570.3

Frequencies

GnomAD3 genomes AF: 0.0000600 AC: 9 AN: 149918 Hom.: 0 Cov.: 0

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

GnomAD2 exomes AF: 0.00 AC: 0 AN: 94 AF XY: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000351 AC: 19 AN: 541806 Hom.: 0 AF XY: 0.0000298 AC XY: 8 AN XY: 268154

African (AFR) AF: 0.000684 AC: 8 AN: 11704

American (AMR) AF: 0.00 AC: 0 AN: 6992

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10446

East Asian (EAS) AF: 0.0000459 AC: 1 AN: 21780

South Asian (SAS) AF: 0.0000447 AC: 1 AN: 22380

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23544

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1774

European-Non Finnish (NFE) AF: 0.0000191 AC: 8 AN: 417832

Other (OTH) AF: 0.0000394 AC: 1 AN: 25354

GnomAD4 genome AF: 0.0000600 AC: 9 AN: 150028 Hom.: 0 Cov.: 0 AF XY: 0.0000820 AC XY: 6 AN XY: 73184

African (AFR) AF: 0.000195 AC: 8 AN: 40958

American (AMR) AF: 0.00 AC: 0 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 4910

South Asian (SAS) AF: 0.00 AC: 0 AN: 4764

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10154

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67324

Other (OTH) AF: 0.000478 AC: 1 AN: 2092

Alfa AF: 0.00 Hom.: 1272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs370049093; hg19: chr13-50070244;