rs17279573

chr4-153659136-A-G

Variant summary

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

The ENST00000502774.1(WDR45P1):n.565A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.149 in 1,598,682 control chromosomes in the GnomAD database, including 19,603 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 0.11 (1281 hom., cov: 33)
  • Exomes 𝑓: 0.15 (18322 hom.)
• Consequence: WDR45P1 ENST00000502774.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.95

Genes affected

WDR45P1 (HGNC:52406): (WD repeat domain 45 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100419170	NR_134873.1	n.355+18119A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR45P1	ENST00000502774.1	n.565A>G		non_coding_transcript_exon_variant	1/1
	ENST00000602666.1	n.355+18119A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17388 AN: 152040 Hom.: 1282 Cov.: 33

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.153 AC: 221323 AN: 1446524 Hom.: 18322 Cov.: 36 AF XY: 0.154 AC XY: 110958 AN XY: 720288

Gnomad4 AFR exome AF: 0.0218

Gnomad4 AMR exome AF: 0.0928

Gnomad4 ASJ exome AF: 0.0817

Gnomad4 EAS exome AF: 0.320

Gnomad4 SAS exome AF: 0.157

Gnomad4 FIN exome AF: 0.0987

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome AF: 0.114 AC: 17382 AN: 152158 Hom.: 1281 Cov.: 33 AF XY: 0.114 AC XY: 8455 AN XY: 74378

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0887

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.129

Alfa AF: 0.124 Hom.: 227

Bravo AF: 0.112

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	12
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17279573; hg19: chr4-154580288;