rs277606

Positions:

• chr9-34785311-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047423102.1(PHF24):​c.133+82273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,094 control chromosomes in the GnomAD database, including 22,520 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (22520 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

Genes affected

PHF24 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF24	XM_047423102.1	c.133+82273T>C		intron_variant
PHF24	XM_047423103.1	c.70+82273T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78064 AN: 151976 Hom.: 22514 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 78080 AN: 152094 Hom.: 22520 Cov.: 32 AF XY: 0.513 AC XY: 38163 AN XY: 74354

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.560

Alfa AF: 0.624 Hom.: 39657

Bravo AF: 0.498

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277606; hg19: chr9-34785308;