chr16-67148096-A-G

Position:

• chr16-67148096-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_025187.5(PHAF1):​c.*965A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,632 control chromosomes in the GnomAD database, including 28,484 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 0.58 (28448 hom., cov: 34)
  • Exomes 𝑓: 0.46 (36 hom.)
• Consequence: PHAF1 NM_025187.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

Genes affected

PHAF1 (HGNC:29564): (phagosome assembly factor 1) Predicted to be involved in Golgi to plasma membrane protein transport. Located in phagophore assembly site. [provided by Alliance of Genome Resources, Apr 2022]

B3GNT9 (HGNC:28714): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9) Predicted to enable UDP-glycosyltransferase activity. Predicted to be involved in poly-N-acetyllactosamine biosynthetic process. Predicted to be integral component of membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHAF1	NM_025187.5	c.*965A>G		3_prime_UTR_variant	16/16	ENST00000219139.8	NP_079463.2
B3GNT9	NM_033309.3	c.*1181T>C		downstream_gene_variant		ENST00000449549.4	NP_171608.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHAF1	ENST00000219139.8	c.*965A>G		3_prime_UTR_variant	16/16	1	NM_025187.5	ENSP00000219139.3
B3GNT9	ENST00000449549.4	c.*1181T>C		downstream_gene_variant		1	NM_033309.3	ENSP00000400157.3

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88000 AN: 152088 Hom.: 28387 Cov.: 34

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.554

GnomAD4 exome AF: 0.462 AC: 197 AN: 426 Hom.: 36 Cov.: 0 AF XY: 0.465 AC XY: 119 AN XY: 256

Gnomad4 FIN exome AF: 0.464

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.579 AC: 88123 AN: 152206 Hom.: 28448 Cov.: 34 AF XY: 0.580 AC XY: 43133 AN XY: 74420

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.558

Alfa AF: 0.463 Hom.: 22553

Bravo AF: 0.588

Asia WGS AF: 0.572 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9033; hg19: chr16-67181999;