rs7071661

chr10-120810472-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.487-33588A>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 0.257 in 152,048 control chromosomes in the GnomAD database, including 5,201 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 0.26 (5201 hom., cov: 32)
• Consequence: WDR11-DT NR_033850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR11-DT	NR_033850.1	n.487-33588A>G		intron_variant, non_coding_transcript_variant
LINC02930	XR_002957103.2	n.401-1559T>C		intron_variant, non_coding_transcript_variant
LINC02930	XR_007062314.1	n.1111-1559T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02930	ENST00000659883.1	n.403-1559T>C		intron_variant, non_coding_transcript_variant
WDR11-DT	ENST00000661416.1	n.104-18546A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39030 AN: 151930 Hom.: 5197 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.257 AC: 39060 AN: 152048 Hom.: 5201 Cov.: 32 AF XY: 0.256 AC XY: 18993 AN XY: 74318

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.269

Alfa AF: 0.249 Hom.: 5218

Bravo AF: 0.253

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.9
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071661; hg19: chr10-122569984;