rs1254167

Variant names:

• chr10-120841691-C-G
• rs1254167
• ENST00000456120.6:n.451+9003G>C

Variant summary

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

The ENST00000456120.6(WDR11-DT):​n.451+9003G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0964 in 152,178 control chromosomes in the GnomAD database, including 738 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 0.096 (738 hom., cov: 33)
• Consequence: WDR11-DT ENST00000456120.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 9 publications found

Genes affected

WDR11-DT (HGNC:27437): (WDR11 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.486+9003G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000456120.6	n.451+9003G>C		intron_variant	Intron 1 of 3	5
WDR11-DT	ENST00000598981.5	n.103+9416G>C		intron_variant	Intron 1 of 3	5
WDR11-DT	ENST00000628194.3	n.670+9003G>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14659 AN: 152060 Hom.: 736 Cov.: 33

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0874

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

GnomAD4 genome AF: 0.0964 AC: 14669 AN: 152178 Hom.: 738 Cov.: 33 AF XY: 0.0952 AC XY: 7080 AN XY: 74398

African (AFR) AF: 0.0903 AC: 3746 AN: 41504

American (AMR) AF: 0.0692 AC: 1056 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 380 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5186

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1667 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7310 AN: 68020

Other (OTH) AF: 0.0874 AC: 185 AN: 2116

Alfa AF: 0.100 Hom.: 91

Bravo AF: 0.0907

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.40
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1254167; hg19: chr10-122601203;