rs2812377

Positions:

• chr9-34710453-A-C
• chr9-34710453-A-T

Variant summary

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

The ENST00000664167.1(ENSG00000288583):​n.86+7415A>C 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 0.292 in 148,846 control chromosomes in the GnomAD database, including 6,762 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 0.29 (6762 hom., cov: 29)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF24	XM_047423102.1	c.133+7415A>C		intron_variant
PHF24	XM_047423103.1	c.70+7415A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664167.1	n.86+7415A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.292 AC: 43394 AN: 148748 Hom.: 6763 Cov.: 29

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.292 AC: 43396 AN: 148846 Hom.: 6762 Cov.: 29 AF XY: 0.293 AC XY: 21185 AN XY: 72266

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.317

Alfa AF: 0.322 Hom.: 12183

Bravo AF: 0.289

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2812377; hg19: chr9-34710450; COSMIC: COSV52398698;