6-63646806-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT

Variant names:

• chr6-63646806-C-CTTT
• rs11285703
• NM_001370348.2:c.244+31_244+33dupTTT

Variant summary

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

The NM_001370348.2(PHF3):​c.244+31_244+33dupTTT 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 0.000071 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00035 (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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF3	NM_001370348.2	c.244+31_244+33dupTTT		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+12insTTT		intron_variant	Intron 2 of 15	5	NM_001370348.2	ENSP00000262043.4

Frequencies

GnomAD3 genomes AF: 0.0000705 AC: 6 AN: 85058 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000124

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000336

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000231

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000348 AC: 323 AN: 927582 Hom.: 0 Cov.: 0 AF XY: 0.000310 AC XY: 137 AN XY: 441920

Gnomad4 AFR exome AF: 0.000467

Gnomad4 AMR exome AF: 0.000102

Gnomad4 ASJ exome AF: 0.000166

Gnomad4 EAS exome AF: 0.000261

Gnomad4 SAS exome AF: 0.000108

Gnomad4 FIN exome AF: 0.000155

Gnomad4 NFE exome AF: 0.000369

Gnomad4 OTH exome AF: 0.000272

GnomAD4 genome AF: 0.0000706 AC: 6 AN: 85040 Hom.: 0 Cov.: 0 AF XY: 0.000102 AC XY: 4 AN XY: 39150

Gnomad4 AFR AF: 0.000140

Gnomad4 AMR AF: 0.000124

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000337

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000231

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;