rs17604662

chr16-72187565-A-G

Variant summary

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

The XM_047434734.1(PMFBP1):c.-863+12835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,232 control chromosomes in the GnomAD database, including 509 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 0.076 (509 hom., cov: 32)
• Consequence: PMFBP1 XM_047434734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

PMFBP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PMFBP1	XM_047434734.1	c.-863+12835T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11539 AN: 152114 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0759 AC: 11553 AN: 152232 Hom.: 509 Cov.: 32 AF XY: 0.0725 AC XY: 5401 AN XY: 74460

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0955 Hom.: 339

Bravo AF: 0.0771

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.8
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17604662; hg19: chr16-72221464;