4-10117121-G-T

Variant names:

• chr4-10117121-G-T
• rs3822259
• ENST00000701208.2:n.84G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000818624.1(ENSG00000289865):​n.105+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,982 control chromosomes in the GnomAD database, including 32,639 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 0.65 (32639 hom., cov: 32)
• Consequence: ENSG00000289865 ENST00000818624.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 8 publications found

Genes affected

ENSG00000289865 (HGNC:58731):

LOC124900666 (HGNC:):

WDR1 (HGNC:12754): (WD repeat domain 1) This gene encodes a protein containing 9 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, mostly including a trp-asp at the C-terminal end. WD domains are involved in protein-protein interactions. The encoded protein may help induce the disassembly of actin filaments. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289865	ENST00000701208.2		n.84G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289865	ENST00000818624.1		n.105+7G>T		splice_region intron	N/A
	ENSG00000289865	ENST00000818625.1		n.59+7G>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98598 AN: 151866 Hom.: 32617 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.649 AC: 98676 AN: 151982 Hom.: 32639 Cov.: 32 AF XY: 0.650 AC XY: 48277 AN XY: 74272

African (AFR) AF: 0.524 AC: 21715 AN: 41466

American (AMR) AF: 0.722 AC: 11031 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2719 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3333 AN: 5146

South Asian (SAS) AF: 0.569 AC: 2746 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7286 AN: 10532

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47417 AN: 67952

Other (OTH) AF: 0.681 AC: 1440 AN: 2114

Alfa AF: 0.582 Hom.: 1688

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.060
DANN	Benign	0.52
PhyloP100		-1.9
PromoterAI		-0.063	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3822259; hg19: chr4-10118745;