rs2997312

Variant names:

• chr10-120808190-G-A
• rs2997312
• ENST00000456120.6:n.560+43C>T

Variant summary

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

The ENST00000628194.3(WDR11-DT):​n.671-31306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,098 control chromosomes in the GnomAD database, including 3,163 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 0.18 (3163 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR11-DT ENST00000628194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628194.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11-DT	NR_033850.1		n.487-31306C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11-DT	ENST00000456120.6	TSL:5	n.560+43C>T		intron	N/A
	WDR11-DT	ENST00000598981.5	TSL:5	n.228+22029C>T		intron	N/A
	WDR11-DT	ENST00000628194.3	TSL:2	n.671-31306C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27178 AN: 151980 Hom.: 3147 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.154

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.179 AC: 27245 AN: 152098 Hom.: 3163 Cov.: 33 AF XY: 0.176 AC XY: 13090 AN XY: 74346

African (AFR) AF: 0.331 AC: 13733 AN: 41458

American (AMR) AF: 0.105 AC: 1611 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.0877 AC: 453 AN: 5164

South Asian (SAS) AF: 0.145 AC: 698 AN: 4818

European-Finnish (FIN) AF: 0.160 AC: 1690 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8161 AN: 68010

Other (OTH) AF: 0.154 AC: 326 AN: 2112

Alfa AF: 0.139 Hom.: 2856

Bravo AF: 0.183

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.34
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2997312;

hg19: chr10-122567702;