chr4-154523606-A-G

Variant names:

• chr4-154523606-A-G
• rs4642230
• ENST00000505711.1:n.120A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR77P1	ENST00000505711.1	n.120A>G		non_coding_transcript_exon_variant	Exon 1 of 2	6

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

African (AFR) AF: 0.967 AC: 578 AN: 598

American (AMR) AF: 0.922 AC: 1201 AN: 1302

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 892 AN: 934

East Asian (EAS) AF: 0.617 AC: 365 AN: 592

South Asian (SAS) AF: 0.934 AC: 8589 AN: 9200

European-Finnish (FIN) AF: 0.917 AC: 1551 AN: 1692

Middle Eastern (MID) AF: 0.938 AC: 332 AN: 354

European-Non Finnish (NFE) AF: 0.922 AC: 32013 AN: 34714

Other (OTH) AF: 0.922 AC: 2022 AN: 2194

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

African (AFR) AF: 0.915 AC: 37819 AN: 41336

American (AMR) AF: 0.802 AC: 12240 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2990 AN: 3464

East Asian (EAS) AF: 0.475 AC: 2396 AN: 5048

South Asian (SAS) AF: 0.823 AC: 3939 AN: 4788

European-Finnish (FIN) AF: 0.776 AC: 8093 AN: 10426

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56098 AN: 67864

Other (OTH) AF: 0.846 AC: 1777 AN: 2100

Alfa AF: 0.823 Hom.: 67192

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
PhyloP100		-5.2

Splicing

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

Other links and lift over

dbSNP: rs4642230; hg19: chr4-155444758;