9-34771856-A-T

Variant names:

• chr9-34771856-A-T
• rs16931907
• ENST00000664167.1:n.87-2183A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664167.1(ENSG00000230074):​n.87-2183A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,212 control chromosomes in the GnomAD database, including 2,106 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 0.13 (2106 hom., cov: 32)
• Consequence: ENSG00000230074 ENST00000664167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 3 publications found

Genes affected

ENSG00000230074 (HGNC:):

PHF24 (HGNC:29180): (PHD finger protein 24) Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+68818A>T		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.70+68818A>T		intron_variant	Intron 2 of 9		XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230074	ENST00000664167.1	n.87-2183A>T		intron_variant	Intron 1 of 1
ENSG00000230074	ENST00000837930.1	n.174+68818A>T		intron_variant	Intron 2 of 3
ENSG00000230074	ENST00000837931.1	n.306+68818A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19980 AN: 152094 Hom.: 2107 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.131 AC: 19980 AN: 152212 Hom.: 2106 Cov.: 32 AF XY: 0.137 AC XY: 10184 AN XY: 74422

African (AFR) AF: 0.0474 AC: 1970 AN: 41572

American (AMR) AF: 0.162 AC: 2479 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3050 AN: 5166

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10580

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9042 AN: 67994

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.121 Hom.: 166

Bravo AF: 0.130

Asia WGS AF: 0.381 AC: 1320 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	13
DANN	Benign	0.81
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs16931907; hg19: chr9-34771853;