6-63646806-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001370348.2(PHF3):c.244+33del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.48 (8513 hom., cov: 0)
  • Exomes 𝑓: 0.34 (677 hom.)
  • Failed GnomAD Quality Control
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -10 ACMG points.

• BP6: Variant 6-63646806-CT-C is Benign according to our data. Variant chr6-63646806-CT-C is described in ClinVar as [Benign]. Clinvar id is 2776132.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF3	NM_001370348.2	c.244+33del		intron_variant		ENST00000262043.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF3	ENST00000262043.8	c.244+33del		intron_variant		5	NM_001370348.2	P1

Frequencies

GnomAD3 genomes AF: 0.484 AC: 41136 AN: 85066 Hom.: 8505 Cov.: 0

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.438

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.432

GnomAD3 exomes AF: 0.00337 AC: 88 AN: 26084 Hom.: 0 AF XY: 0.00213 AC XY: 31 AN XY: 14534

Gnomad AFR exome AF: 0.00445

Gnomad AMR exome AF: 0.00148

Gnomad ASJ exome AF: 0.0150

Gnomad EAS exome AF: 0.00269

Gnomad SAS exome AF: 0.00195

Gnomad FIN exome AF: 0.00712

Gnomad NFE exome AF: 0.00300

Gnomad OTH exome AF: 0.00415

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.343 AC: 313748 AN: 914414 Hom.: 677 Cov.: 0 AF XY: 0.341 AC XY: 148744 AN XY: 435712

Gnomad4 AFR exome AF: 0.361

Gnomad4 AMR exome AF: 0.242

Gnomad4 ASJ exome AF: 0.332

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.329

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.347

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome AF: 0.484 AC: 41129 AN: 85048 Hom.: 8513 Cov.: 0 AF XY: 0.479 AC XY: 18734 AN XY: 39150

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.429

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 02, 2024

- -

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;