16-72151102-G-A

Position:

• chr16-72151102-G-A

Variant summary

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

The NM_031293.3(PMFBP1):​c.415-273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,090 control chromosomes in the GnomAD database, including 28,077 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 0.60 (28077 hom., cov: 33)
• Consequence: PMFBP1 NM_031293.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

Genes affected

PMFBP1 (HGNC:17728): (polyamine modulated factor 1 binding protein 1) Involved in spermatogenesis. Located in sperm connecting piece. Implicated in spermatogenic failure 31. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMFBP1	NM_031293.3	c.415-273C>T		intron_variant		ENST00000237353.15	NP_112583.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PMFBP1	ENST00000237353.15	c.415-273C>T		intron_variant		1	NM_031293.3	ENSP00000237353

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90793 AN: 151972 Hom.: 28041 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.597 AC: 90867 AN: 152090 Hom.: 28077 Cov.: 33 AF XY: 0.595 AC XY: 44206 AN XY: 74334

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.590

Alfa AF: 0.569 Hom.: 11523

Bravo AF: 0.590

Asia WGS AF: 0.488 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3852784; hg19: chr16-72185001;