rs2812378

chr9-34710263-G-Achr9-34710263-G-C

Variant summary

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

The ENST00000664167.1(ENSG00000288583):n.86+7225G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 592,598 control chromosomes in the GnomAD database, including 140,475 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 0.67 (34177 hom., cov: 31)
  • Exomes 𝑓: 0.69 (106298 hom.)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF24	XM_047423102.1	c.133+7225G>A		intron_variant
PHF24	XM_047423103.1	c.70+7225G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664167.1	n.86+7225G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101177 AN: 151924 Hom.: 34168 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.697

GnomAD4 exome AF: 0.689 AC: 303746 AN: 440552 Hom.: 106298 AF XY: 0.689 AC XY: 159386 AN XY: 231340

Gnomad4 AFR exome AF: 0.587

Gnomad4 AMR exome AF: 0.715

Gnomad4 ASJ exome AF: 0.724

Gnomad4 EAS exome AF: 0.948

Gnomad4 SAS exome AF: 0.655

Gnomad4 FIN exome AF: 0.722

Gnomad4 NFE exome AF: 0.663

Gnomad4 OTH exome AF: 0.688

GnomAD4 genome AF: 0.666 AC: 101223 AN: 152046 Hom.: 34177 Cov.: 31 AF XY: 0.671 AC XY: 49885 AN XY: 74308

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.700

Alfa AF: 0.670 Hom.: 34156

Bravo AF: 0.661

Asia WGS AF: 0.778 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.96
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2812378; hg19: chr9-34710260; COSMIC: COSV52398692;