6-63646806-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTT

Variant names:

• chr6-63646806-C-CT
• rs11285703
• NM_001370348.2:c.244+33dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001370348.2(PHF3):​c.244+33dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.011 (12 hom., cov: 0)
  • Exomes 𝑓: 0.032 (0 hom.)
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0111 (942/85034) while in subpopulation AFR AF= 0.0301 (646/21458). AF 95% confidence interval is 0.0282. There are 12 homozygotes in gnomad4. There are 404 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF3	NM_001370348.2	c.244+33dupT		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+11_244+12insT		intron_variant	Intron 2 of 15	5	NM_001370348.2	ENSP00000262043.4

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 941 AN: 85052 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00435

Gnomad ASJ AF: 0.000421

Gnomad EAS AF: 0.00773

Gnomad SAS AF: 0.00561

Gnomad FIN AF: 0.00220

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00469

Gnomad OTH AF: 0.0137

GnomAD3 exomes AF: 0.000153 AC: 4 AN: 26084 Hom.: 0 AF XY: 0.000138 AC XY: 2 AN XY: 14534

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00215

Gnomad EAS exome AF: 0.000538

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000133

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0322 AC: 29587 AN: 918932 Hom.: 0 Cov.: 0 AF XY: 0.0318 AC XY: 13915 AN XY: 437890

Gnomad4 AFR exome AF: 0.0279

Gnomad4 AMR exome AF: 0.0115

Gnomad4 ASJ exome AF: 0.0254

Gnomad4 EAS exome AF: 0.0278

Gnomad4 SAS exome AF: 0.0270

Gnomad4 FIN exome AF: 0.0227

Gnomad4 NFE exome AF: 0.0333

Gnomad4 OTH exome AF: 0.0291

GnomAD4 genome AF: 0.0111 AC: 942 AN: 85034 Hom.: 12 Cov.: 0 AF XY: 0.0103 AC XY: 404 AN XY: 39144

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.00435

Gnomad4 ASJ AF: 0.000421

Gnomad4 EAS AF: 0.00776

Gnomad4 SAS AF: 0.00565

Gnomad4 FIN AF: 0.00220

Gnomad4 NFE AF: 0.00469

Gnomad4 OTH AF: 0.0136

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;