chr10-120850879-C-G

Variant names:

• chr10-120850879-C-G
• rs10886785
• ENST00000456120.6:n.266G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000628194.3(WDR11-DT):​n.485G>C 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 0.158 in 159,032 control chromosomes in the GnomAD database, including 2,620 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2457 hom., cov: 33)
  • Exomes 𝑓: 0.19 (163 hom.)
• Consequence: WDR11-DT ENST00000628194.3 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0860
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-120850879-C-G is Benign according to our data. Variant chr10-120850879-C-G is described in ClinVar as Benign. ClinVar VariationId is 1233113.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628194.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11-DT	NR_033850.1		n.301G>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11-DT	ENST00000456120.6	TSL:5	n.266G>C		non_coding_transcript_exon	Exon 1 of 4
	WDR11-DT	ENST00000628194.3	TSL:2	n.485G>C		non_coding_transcript_exon	Exon 1 of 3
	WDR11-DT	ENST00000598981.5	TSL:5	n.103+228G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23891 AN: 152158 Hom.: 2456 Cov.: 33

Gnomad AFR AF: 0.0505

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.187 AC: 1266 AN: 6756 Hom.: 163 Cov.: 0 AF XY: 0.188 AC XY: 641 AN XY: 3410

African (AFR) AF: 0.0400 AC: 2 AN: 50

American (AMR) AF: 0.325 AC: 364 AN: 1120

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 12 AN: 56

East Asian (EAS) AF: 0.256 AC: 44 AN: 172

South Asian (SAS) AF: 0.132 AC: 88 AN: 668

European-Finnish (FIN) AF: 0.0714 AC: 12 AN: 168

Middle Eastern (MID) AF: 0.125 AC: 2 AN: 16

European-Non Finnish (NFE) AF: 0.165 AC: 692 AN: 4184

Other (OTH) AF: 0.155 AC: 50 AN: 322

GnomAD4 genome AF: 0.157 AC: 23884 AN: 152276 Hom.: 2457 Cov.: 33 AF XY: 0.157 AC XY: 11680 AN XY: 74460

African (AFR) AF: 0.0503 AC: 2092 AN: 41562

American (AMR) AF: 0.277 AC: 4238 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1770 AN: 5184

South Asian (SAS) AF: 0.157 AC: 758 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1281 AN: 10606

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12515 AN: 68010

Other (OTH) AF: 0.151 AC: 319 AN: 2114

Alfa AF: 0.167 Hom.: 327

Bravo AF: 0.167

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.26
PhyloP100		0.086
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10886785; hg19: chr10-122610391;