rs811047

Positions:

• chr16-72226794-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

PMFBP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PMFBP1	XM_047434734.1	c.-1011+22369C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.567

Alfa AF: 0.591 Hom.: 54179

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs811047; hg19: chr16-72260693;