rs3852784

Variant names:

• chr16-72151102-G-A
• rs3852784
• NM_031293.3:c.415-273C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-72151102-G-A
• chr16-72151102-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

PMFBP1 Gene-Disease associations (from GenCC):

• spermatogenic failure 31

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PMFBP1	NM_031293.3	c.415-273C>T		intron_variant	Intron 4 of 20	ENST00000237353.15	NP_112583.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMFBP1	ENST00000237353.15	c.415-273C>T		intron_variant	Intron 4 of 20	1	NM_031293.3	ENSP00000237353.10

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

African (AFR) AF: 0.748 AC: 31033 AN: 41492

American (AMR) AF: 0.465 AC: 7101 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2254 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1790 AN: 5166

South Asian (SAS) AF: 0.625 AC: 3011 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5933 AN: 10576

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37942 AN: 67980

Other (OTH) AF: 0.590 AC: 1247 AN: 2112

Alfa AF: 0.570 Hom.: 12990

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
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3852784; hg19: chr16-72185001;