chr9-34710341-G-A

Position:

• chr9-34710341-G-A

Variant summary

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

The ENST00000664167.1(ENSG00000288583):​n.86+7303G>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 0.242 in 152,008 control chromosomes in the GnomAD database, including 5,343 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 0.24 (5343 hom., cov: 32)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF24	XM_047423102.1	c.133+7303G>A		intron_variant
PHF24	XM_047423103.1	c.70+7303G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664167.1	n.86+7303G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36761 AN: 151890 Hom.: 5343 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.242 AC: 36777 AN: 152008 Hom.: 5343 Cov.: 32 AF XY: 0.240 AC XY: 17796 AN XY: 74270

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.230

Alfa AF: 0.312 Hom.: 10199

Bravo AF: 0.233

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11574914; hg19: chr9-34710338;