6-63646806-CTTTTTTTTTTTTTT-CTTT

Variant names:

• chr6-63646806-CTTTTTTTTTTT-C
• rs11285703
• NM_001370348.2:c.244+23_244+33delTTTTTTTTTTT

Variant summary

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

The NM_001370348.2(PHF3):​c.244+23_244+33delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000323 in 928,472 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: not found (cov: 0)
  • Exomes 𝑓: 0.0000032 (0 hom.)
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23
• Publications: 0 publications found

Genes affected

PHF3 (HGNC:8921): (PHD finger protein 3) This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370348.2. 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
	PHF3	NM_001370348.2	MANE Select	c.244+23_244+33delTTTTTTTTTTT		intron	N/A	NP_001357277.1	Q92576-1
	PHF3	NM_015153.4		c.244+23_244+33delTTTTTTTTTTT		intron	N/A	NP_055968.1	Q92576-1
	PHF3	NM_001290259.2		c.-214+23_-214+33delTTTTTTTTTTT		intron	N/A	NP_001277188.1	Q92576-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF3	ENST00000262043.8	TSL:5 MANE Select	c.244+12_244+22delTTTTTTTTTTT		intron	N/A	ENSP00000262043.4	Q92576-1
	PHF3	ENST00000393387.5	TSL:1	c.244+12_244+22delTTTTTTTTTTT		intron	N/A	ENSP00000377048.1	Q92576-1
	PHF3	ENST00000506783.5	TSL:1	c.-153+10657_-153+10667delTTTTTTTTTTT		intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000323 AC: 3 AN: 928472 Hom.: 0 AF XY: 0.00000226 AC XY: 1 AN XY: 442354

African (AFR) AF: 0.00 AC: 0 AN: 19272

American (AMR) AF: 0.00 AC: 0 AN: 9848

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12030

East Asian (EAS) AF: 0.00 AC: 0 AN: 22996

South Asian (SAS) AF: 0.00 AC: 0 AN: 18570

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2434

European-Non Finnish (NFE) AF: 0.00000381 AC: 3 AN: 787138

Other (OTH) AF: 0.00 AC: 0 AN: 36818

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs11285703; hg19: chr6-64356711;