9-34768696-C-T

Variant summary

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

The ENST00000664167.1(ENSG00000288583):n.87-5343C>T 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 0.173 in 152,138 control chromosomes in the GnomAD database, including 3,064 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 0.17 (3064 hom., cov: 32)
• Consequence: ENST00000664167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF24	XM_047423102.1	c.133+65658C>T		intron_variant
PHF24	XM_047423103.1	c.70+65658C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664167.1	n.87-5343C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26398 AN: 152018 Hom.: 3065 Cov.: 32

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.173 AC: 26388 AN: 152138 Hom.: 3064 Cov.: 32 AF XY: 0.167 AC XY: 12447 AN XY: 74372

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.206

Alfa AF: 0.238 Hom.: 6175

Bravo AF: 0.169

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.28
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13293020; hg19: chr9-34768693; COSMIC: COSV60353204;