rs1007572113

Variant names:

• chr9-93576755-GGCGGC-G
• rs1007572113
• NM_005392.4:c.-8_-4delGCGGC

Your query was ambiguous. Multiple possible variants found:

• chr9-93576755-GGCGGC-G
• chr9-93576755-GGCGGC-GGCGGCGCGGC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005392.4(PHF2):​c.-8_-4delGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000195 in 1,025,814 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: PHF2 NM_005392.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 0 publications found

Genes affected

PHF2 (HGNC:8920): (PHD finger protein 2) This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005392.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF2	NM_005392.4	MANE Select	c.-8_-4delGCGGC		5_prime_UTR	Exon 1 of 22	NP_005383.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF2	ENST00000359246.9	TSL:1 MANE Select	c.-8_-4delGCGGC		5_prime_UTR	Exon 1 of 22	ENSP00000352185.4	O75151
	PHF2	ENST00000851896.1		c.-8_-4delGCGGC		5_prime_UTR	Exon 1 of 22	ENSP00000521955.1
	PHF2	ENST00000937581.1		c.-8_-4delGCGGC		5_prime_UTR	Exon 1 of 22	ENSP00000607640.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD2 exomes AF: 0.00 AC: 0 AN: 88968 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000195 AC: 2 AN: 1025814 Hom.: 0 AF XY: 0.00000199 AC XY: 1 AN XY: 503726

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 19602

American (AMR) AF: 0.00 AC: 0 AN: 18482

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12508

East Asian (EAS) AF: 0.00 AC: 0 AN: 5870

South Asian (SAS) AF: 0.00 AC: 0 AN: 64502

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14518

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3038

European-Non Finnish (NFE) AF: 0.00000235 AC: 2 AN: 851722

Other (OTH) AF: 0.00 AC: 0 AN: 35572

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs1007572113; hg19: chr9-96339037;