chr16-72190436-C-T

Variant names:

• chr16-72190436-C-T
• rs12918956
• XM_047434734.1:c.-863+9964G>A

Variant summary

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

The XM_047434734.1(PMFBP1):​c.-863+9964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,098 control chromosomes in the GnomAD database, including 23,020 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 0.55 (23020 hom., cov: 33)
• Consequence: PMFBP1 XM_047434734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMFBP1	XM_047434734.1	c.-863+9964G>A		intron_variant	Intron 3 of 23		XP_047290690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.546 AC: 83031 AN: 151980 Hom.: 22995 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.546 AC: 83103 AN: 152098 Hom.: 23020 Cov.: 33 AF XY: 0.544 AC XY: 40448 AN XY: 74354

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.544

Alfa AF: 0.539 Hom.: 11339

Bravo AF: 0.537

Asia WGS AF: 0.505 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12918956; hg19: chr16-72224335;