ENST00000456120.6:n.560+3852C>A

Variant names:

• chr10-120804381-G-T
• rs7092824
• ENST00000456120.6:n.560+3852C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000456120.6(WDR11-DT):​n.560+3852C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,066 control chromosomes in the GnomAD database, including 36,726 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 (36726 hom., cov: 33)
• Consequence: WDR11-DT ENST00000456120.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.487-27497C>A		intron_variant	Intron 1 of 2
LINC02930	XR_002957103.2	n.401-7650G>T		intron_variant	Intron 2 of 4
LINC02930	XR_007062314.1	n.1111-7650G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000456120.6	n.560+3852C>A		intron_variant	Intron 2 of 3	5
WDR11-DT	ENST00000598981.5	n.228+25838C>A		intron_variant	Intron 2 of 3	5
WDR11-DT	ENST00000628194.3	n.671-27497C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104363 AN: 151948 Hom.: 36723 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.687 AC: 104396 AN: 152066 Hom.: 36726 Cov.: 33 AF XY: 0.688 AC XY: 51113 AN XY: 74338

African (AFR) AF: 0.520 AC: 21550 AN: 41430

American (AMR) AF: 0.728 AC: 11130 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3468

East Asian (EAS) AF: 0.711 AC: 3683 AN: 5178

South Asian (SAS) AF: 0.619 AC: 2987 AN: 4822

European-Finnish (FIN) AF: 0.740 AC: 7831 AN: 10578

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

European-Non Finnish (NFE) AF: 0.771 AC: 52390 AN: 67990

Other (OTH) AF: 0.695 AC: 1468 AN: 2112

Alfa AF: 0.741 Hom.: 24834

Bravo AF: 0.677

Asia WGS AF: 0.650 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs7092824; hg19: chr10-122563893;