rs7071661

Variant names:

• chr10-120810472-T-C
• rs7071661
• ENST00000456120.6:n.452-2131A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456120.6(WDR11-DT):​n.452-2131A>G variant causes a intron 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 ENST00000456120.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 2 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 -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 rank	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.487-33588A>G		intron_variant	Intron 1 of 2
LINC02930	XR_002957103.2	n.401-1559T>C		intron_variant	Intron 2 of 4
LINC02930	XR_007062314.1	n.1111-1559T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000456120.6	n.452-2131A>G		intron_variant	Intron 1 of 3	5
WDR11-DT	ENST00000598981.5	n.228+19747A>G		intron_variant	Intron 2 of 3	5
WDR11-DT	ENST00000628194.3	n.671-33588A>G		intron_variant	Intron 1 of 2	2

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

African (AFR) AF: 0.319 AC: 13239 AN: 41466

American (AMR) AF: 0.192 AC: 2933 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 880 AN: 3472

East Asian (EAS) AF: 0.0791 AC: 409 AN: 5168

South Asian (SAS) AF: 0.173 AC: 830 AN: 4804

European-Finnish (FIN) AF: 0.276 AC: 2915 AN: 10574

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16904 AN: 67966

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.251 Hom.: 7742

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs7071661; hg19: chr10-122569984;