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 ENST00000701208.2(ENSG00000289865):​n.84G>T 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 0.649 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 ENST00000701208.2 non_coding_transcript_exon
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900666	XR_007058030.1	n.33G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289865	ENST00000701208.2	n.84G>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289865	ENST00000818624.1	n.105+7G>T		splice_region_variant, intron_variant	Intron 1 of 2
ENSG00000289865	ENST00000818625.1	n.59+7G>T		splice_region_variant, intron_variant	Intron 1 of 3

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 v4.3

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;