rs10972206

Positions:

• chr9-34713528-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000664167.1(ENSG00000288583):​n.86+10490A>G 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 0.00792 in 152,090 control chromosomes in the GnomAD database, including 9 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 0.0079 (9 hom., cov: 32)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+10490A>G		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+10490A>G		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664167.1	n.86+10490A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00792 AC: 1203 AN: 151972 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00388

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.00432

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

GnomAD4 genome AF: 0.00792 AC: 1205 AN: 152090 Hom.: 9 Cov.: 32 AF XY: 0.00710 AC XY: 528 AN XY: 74346

Gnomad4 AFR AF: 0.00256

Gnomad4 AMR AF: 0.00557

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.00457

Gnomad4 FIN AF: 0.00388

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.00428

Alfa AF: 0.00995 Hom.: 1

Bravo AF: 0.00783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10972206; hg19: chr9-34713525;