10-120809370-T-C

Variant names:

• chr10-120809370-T-C
• rs10788123
• ENST00000456120.6:n.452-1029A>G

Variant summary

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

The ENST00000456120.6(WDR11-DT):​n.452-1029A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,056 control chromosomes in the GnomAD database, including 37,309 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 0.69 (37309 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: WDR11-DT ENST00000456120.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 9 publications found

Genes affected

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

LINC02930 (HGNC:55821): (long intergenic non-protein coding RNA 2930)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456120.6. 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
	WDR11-DT	NR_033850.1		n.487-32486A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11-DT	ENST00000456120.6	TSL:5	n.452-1029A>G		intron	N/A
	WDR11-DT	ENST00000598981.5	TSL:5	n.228+20849A>G		intron	N/A
	WDR11-DT	ENST00000628194.3	TSL:2	n.671-32486A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105449 AN: 151940 Hom.: 37311 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.694 AC: 105480 AN: 152056 Hom.: 37309 Cov.: 33 AF XY: 0.695 AC XY: 51638 AN XY: 74348

African (AFR) AF: 0.547 AC: 22670 AN: 41448

American (AMR) AF: 0.731 AC: 11165 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2601 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3673 AN: 5168

South Asian (SAS) AF: 0.618 AC: 2984 AN: 4828

European-Finnish (FIN) AF: 0.740 AC: 7811 AN: 10560

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52336 AN: 67984

Other (OTH) AF: 0.701 AC: 1480 AN: 2110

Alfa AF: 0.739 Hom.: 111752

Bravo AF: 0.686

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.43
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10788123; hg19: chr10-122568882;