rs2919009

Positions:

• chr10-120831861-C-T

Variant summary

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

The NR_033850.1(WDR11-DT):​n.486+18833G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,122 control chromosomes in the GnomAD database, including 3,618 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 0.21 (3618 hom., cov: 32)
• Consequence: WDR11-DT NR_033850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR11-DT	NR_033850.1	n.486+18833G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR11-DT	ENST00000661416.1	n.103+19246G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32503 AN: 152004 Hom.: 3609 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.214 AC: 32530 AN: 152122 Hom.: 3618 Cov.: 32 AF XY: 0.211 AC XY: 15728 AN XY: 74390

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.233

Alfa AF: 0.219 Hom.: 5078

Bravo AF: 0.214

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2919009; hg19: chr10-122591373;