chr16-72186474-G-C

Position:

• chr16-72186474-G-C

Variant summary

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

The XM_047434734.1(PMFBP1):​c.-862-12404C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,924 control chromosomes in the GnomAD database, including 5,832 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 0.27 (5832 hom., cov: 31)
• Consequence: PMFBP1 XM_047434734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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 (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMFBP1	XM_047434734.1	c.-862-12404C>G		intron_variant			XP_047290690.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40364 AN: 151804 Hom.: 5827 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.266 AC: 40402 AN: 151924 Hom.: 5832 Cov.: 31 AF XY: 0.266 AC XY: 19735 AN XY: 74250

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.274

Alfa AF: 0.221 Hom.: 2113

Bravo AF: 0.268

Asia WGS AF: 0.337 AC: 1175 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	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7186908; hg19: chr16-72220373;