10-120804381-G-T

Position:

• chr10-120804381-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_033850.1(WDR11-DT):​n.487-27497C>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 0.687 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 NR_033850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

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 -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/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.487-27497C>A		intron_variant, non_coding_transcript_variant
LINC02930	XR_002957103.2	n.401-7650G>T		intron_variant, non_coding_transcript_variant
LINC02930	XR_007062314.1	n.1111-7650G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000659883.1	n.403-7650G>T		intron_variant, non_coding_transcript_variant
WDR11-DT	ENST00000661416.1	n.104-12455C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.695

Alfa AF: 0.742 Hom.: 22536

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7092824; hg19: chr10-122563893;