10-120809370-T-C

Position:

• chr10-120809370-T-C

Variant summary

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

The NR_033850.1(WDR11-DT):​n.487-32486A>G 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 0.694 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 NR_033850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.487-32486A>G		intron_variant, non_coding_transcript_variant
LINC02930	XR_002957103.2	n.401-2661T>C		intron_variant, non_coding_transcript_variant
LINC02930	XR_007062314.1	n.1111-2661T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000659883.1	n.403-2661T>C		intron_variant, non_coding_transcript_variant
WDR11-DT	ENST00000661416.1	n.104-17444A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.701

Alfa AF: 0.754 Hom.: 71313

Bravo AF: 0.686

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788123; hg19: chr10-122568882;