rs17618203

Positions:

• chr16-67113107-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_025187.5(PHAF1):​c.64+2868G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,330 control chromosomes in the GnomAD database, including 58 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 0.024 (58 hom., cov: 31)
• Consequence: PHAF1 NM_025187.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3606/152330) while in subpopulation NFE AF= 0.0327 (2223/68038). AF 95% confidence interval is 0.0315. There are 58 homozygotes in gnomad4. There are 1716 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 58 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHAF1	NM_025187.5	c.64+2868G>A		intron_variant		ENST00000219139.8	NP_079463.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHAF1	ENST00000219139.8	c.64+2868G>A		intron_variant		1	NM_025187.5	ENSP00000219139	P1

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3600 AN: 152212 Hom.: 58 Cov.: 31

Gnomad AFR AF: 0.00608

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0321

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.0172

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0237 AC: 3606 AN: 152330 Hom.: 58 Cov.: 31 AF XY: 0.0230 AC XY: 1716 AN XY: 74490

Gnomad4 AFR AF: 0.00606

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.0172

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0280 Hom.: 10

Bravo AF: 0.0249

Asia WGS AF: 0.0290 AC: 101 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	3.7
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17618203; hg19: chr16-67147010;