rs17668704

Positions:

• chr16-72223800-A-T

Variant summary

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

The XM_047434734.1(PMFBP1):​c.-1010-23253T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,078 control chromosomes in the GnomAD database, including 8,700 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 0.33 (8700 hom., cov: 32)
• Consequence: PMFBP1 XM_047434734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

PMFBP1 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMFBP1	XM_047434734.1	c.-1010-23253T>A		intron_variant			XP_047290690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50071 AN: 151960 Hom.: 8674 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.330 AC: 50145 AN: 152078 Hom.: 8700 Cov.: 32 AF XY: 0.333 AC XY: 24772 AN XY: 74348

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.314

Alfa AF: 0.325 Hom.: 1011

Bravo AF: 0.311

Asia WGS AF: 0.302 AC: 1050 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	3.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17668704; hg19: chr16-72257699;