9-34825306-G-A

Position:

• chr9-34825306-G-A

Variant summary

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

The ENST00000658462.1(ENSG00000287368):​n.140+15147G>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 0.53 in 151,772 control chromosomes in the GnomAD database, including 23,153 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 0.53 (23153 hom., cov: 29)
• Consequence: ENST00000658462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.134-64273G>A		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.71-64273G>A		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658462.1	n.140+15147G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80470 AN: 151656 Hom.: 23146 Cov.: 29

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.530 AC: 80498 AN: 151772 Hom.: 23153 Cov.: 29 AF XY: 0.529 AC XY: 39209 AN XY: 74178

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.574

Alfa AF: 0.590 Hom.: 3480

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10758278; hg19: chr9-34825303;