rs811047

Variant names:

• chr16-72226794-G-A
• rs811047
• XM_047434734.1:c.-1011+22369C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-72226794-G-A
• chr16-72226794-G-C
• chr16-72226794-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047434734.1(PMFBP1):​c.-1011+22369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,870 control chromosomes in the GnomAD database, including 22,158 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 0.52 (22158 hom., cov: 32)
• Consequence: PMFBP1 XM_047434734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMFBP1	XM_047434734.1	c.-1011+22369C>T		intron_variant	Intron 2 of 23		XP_047290690.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79675 AN: 151752 Hom.: 22151 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.525 AC: 79696 AN: 151870 Hom.: 22158 Cov.: 32 AF XY: 0.525 AC XY: 38948 AN XY: 74220

African (AFR) AF: 0.332 AC: 13717 AN: 41366

American (AMR) AF: 0.644 AC: 9836 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2031 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3875 AN: 5168

South Asian (SAS) AF: 0.458 AC: 2196 AN: 4800

European-Finnish (FIN) AF: 0.548 AC: 5768 AN: 10516

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40464 AN: 67956

Other (OTH) AF: 0.567 AC: 1199 AN: 2114

Alfa AF: 0.581 Hom.: 115619

Bravo AF: 0.529

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.66
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs811047; hg19: chr16-72260693;