3-52423096-A-T

Variant names:

• chr3-52423096-A-T
• rs752691155
• NM_016483.7:c.925A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016483.7(PHF7):​c.925A>T​(p.Ile309Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PHF7 NM_016483.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

PHF7 (HGNC:18458): (PHD finger protein 7) Spermatogenesis is a complex process regulated by extracellular and intracellular factors as well as cellular interactions among interstitial cells of the testis, Sertoli cells, and germ cells. This gene is expressed in the testis in Sertoli cells but not germ cells. The protein encoded by this gene contains plant homeodomain (PHD) finger domains, also known as leukemia associated protein (LAP) domains, believed to be involved in transcriptional regulation. The protein, which localizes to the nucleus of transfected cells, has been implicated in the transcriptional regulation of spermatogenesis. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04117179).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF7	NM_016483.7	c.925A>T	p.Ile309Leu	missense_variant	Exon 11 of 11	ENST00000327906.8	NP_057567.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF7	ENST00000327906.8	c.925A>T	p.Ile309Leu	missense_variant	Exon 11 of 11	1	NM_016483.7	ENSP00000333024.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.064
BayesDel_addAF	Benign	-0.029	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	6.7
DANN	Benign	0.83
DEOGEN2	Benign	0.0095	T;.;.
Eigen	Benign	-0.97
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.049	N
LIST_S2	Benign	0.65	T;.;T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.041	T;T;T
MetaSVM	Benign	-0.58	T
MutationAssessor	Benign	0.69	N;.;.
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.12	N;N;.
REVEL	Benign	0.23
Sift	Benign	0.22	T;T;.
Sift4G	Benign	0.37	T;T;T
Polyphen		0.0030	B;.;.
Vest4		0.099
MutPred		0.14		Gain of glycosylation at Y308 (P = 0.0075);.;.;
MVP		0.58
MPC		0.24
ClinPred		0.032	T
GERP RS		0.19
Varity_R		0.068
gMVP		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs752691155; hg19: chr3-52457112;