6-63646806-CTTTTTTTTTTTTT-CTTTTTTTTTTT

Variant names:

• chr6-63646806-CTT-C
• rs11285703
• NM_001370348.2:c.244+32_244+33delTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001370348.2(PHF3):​c.244+32_244+33delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 979,352 control chromosomes in the GnomAD database, including 85 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.027 (76 hom., cov: 0)
  • Exomes 𝑓: 0.15 (9 hom.)
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF3	NM_001370348.2	c.244+32_244+33delTT		intron_variant	Intron 2 of 15	ENST00000262043.8	NP_001357277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF3	ENST00000262043.8	c.244+12_244+13delTT		intron_variant	Intron 2 of 15	5	NM_001370348.2	ENSP00000262043.4

Frequencies

GnomAD3 genomes AF: 0.0265 AC: 2254 AN: 85114 Hom.: 76 Cov.: 0

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0159

Gnomad ASJ AF: 0.00758

Gnomad EAS AF: 0.00101

Gnomad SAS AF: 0.000864

Gnomad FIN AF: 0.00146

Gnomad MID AF: 0.0234

Gnomad NFE AF: 0.00339

Gnomad OTH AF: 0.0164

GnomAD3 exomes AF: 0.00219 AC: 57 AN: 26084 Hom.: 0 AF XY: 0.00103 AC XY: 15 AN XY: 14534

Gnomad AFR exome AF: 0.00162

Gnomad AMR exome AF: 0.000740

Gnomad ASJ exome AF: 0.0107

Gnomad EAS exome AF: 0.00108

Gnomad SAS exome AF: 0.00326

Gnomad FIN exome AF: 0.00323

Gnomad NFE exome AF: 0.00206

Gnomad OTH exome AF: 0.00622

GnomAD4 exome AF: 0.152 AC: 135576 AN: 894256 Hom.: 9 AF XY: 0.151 AC XY: 64309 AN XY: 426156

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.142

Gnomad4 ASJ exome AF: 0.173

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.0265 AC: 2256 AN: 85096 Hom.: 76 Cov.: 0 AF XY: 0.0267 AC XY: 1048 AN XY: 39184

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.0159

Gnomad4 ASJ AF: 0.00758

Gnomad4 EAS AF: 0.00101

Gnomad4 SAS AF: 0.000870

Gnomad4 FIN AF: 0.00146

Gnomad4 NFE AF: 0.00340

Gnomad4 OTH AF: 0.0163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs11285703; hg19: chr6-64356711;