rs4642230

Positions:

• chr4-154523606-A-G

Variant summary

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

The ENST00000505711.1(WDR77P1):​n.120A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 203,066 control chromosomes in the GnomAD database, including 75,117 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 0.83 (53196 hom., cov: 27)
  • Exomes 𝑓: 0.92 (21921 hom.)
• Consequence: WDR77P1 ENST00000505711.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.22

Genes affected

WDR77P1 (HGNC:56815): (WDR77 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR77P1	ENST00000505711.1	n.120A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126143 AN: 151368 Hom.: 53146 Cov.: 27

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.846

GnomAD4 exome AF: 0.922 AC: 47543 AN: 51580 Hom.: 21921 Cov.: 0 AF XY: 0.919 AC XY: 31521 AN XY: 34290

Gnomad4 AFR exome AF: 0.967

Gnomad4 AMR exome AF: 0.922

Gnomad4 ASJ exome AF: 0.955

Gnomad4 EAS exome AF: 0.617

Gnomad4 SAS exome AF: 0.934

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.922

Gnomad4 OTH exome AF: 0.922

GnomAD4 genome AF: 0.833 AC: 126249 AN: 151486 Hom.: 53196 Cov.: 27 AF XY: 0.828 AC XY: 61274 AN XY: 73964

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.846

Alfa AF: 0.840 Hom.: 6944

Bravo AF: 0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.079

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4642230; hg19: chr4-155444758;