Genetic Variant PHAF1:c.*965A>G (chr16-67148096-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.31

Publications

47 publications found

Variant links:

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]

PHAF1 links:

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]

B3GNT9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025187.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PHAF1	NM_025187.5	MANE Select	c.*965A>G	3_prime_UTR	Exon 16 of 16	NP_079463.2
PHAF1	NM_001320540.2		c.*965A>G	3_prime_UTR	Exon 17 of 17	NP_001307469.1
PHAF1	NM_001320541.2		c.*965A>G	3_prime_UTR	Exon 17 of 17	NP_001307470.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHAF1	ENST00000219139.8	TSL:1 MANE Select	c.*965A>G		3_prime_UTR	Exon 16 of 16	ENSP00000219139.3
	B3GNT9	ENST00000449549.4	TSL:1 MANE Select	c.*1181T>C		downstream_gene	N/A	ENSP00000400157.3

Frequencies

GnomAD3 genomes

AF:

0.579

AC:

88000

AN:

152088

Hom.:

28387

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.465

AC XY:

119

AN XY:

256

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.464

AC:

195

AN:

420

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.579

AC:

88123

AN:

152206

Hom.:

28448

Cov.:

AF XY:

0.580

AC XY:

43133

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.887

AC:

36870

AN:

41558

American (AMR)

AF:

0.492

AC:

7532

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.529

AC:

1837

AN:

3470

East Asian (EAS)

AF:

0.406

AC:

2100

AN:

5178

South Asian (SAS)

AF:

0.541

AC:

2609

AN:

4820

European-Finnish (FIN)

AF:

0.480

AC:

5091

AN:

10596

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.445

AC:

30225

AN:

67974

Other (OTH)

AF:

0.558

AC:

1175

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1690

3380

5070

6760

8450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.475

Hom.:

38063

Bravo

AF:

0.588

Asia WGS

AF:

0.572

AC:

1993

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

2.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over