rs73027451

Variant names:

• chr19-37885026-C-A
• NM_001291088.2:c.8645G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-37885026-C-A
• chr19-37885026-C-G
• chr19-37885026-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001291088.2(WDR87):​c.8645G>T​(p.Arg2882Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR87 NM_001291088.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.952

Genes affected

WDR87 (HGNC:29934): (WD repeat domain 87)

LOC105372395 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10549915).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR87	NM_001291088.2	c.8645G>T	p.Arg2882Leu	missense_variant	Exon 6 of 6	ENST00000447313.7	NP_001278017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR87	ENST00000447313.7	c.8645G>T	p.Arg2882Leu	missense_variant	Exon 6 of 6	2	NM_001291088.2	ENSP00000405012.2
WDR87	ENST00000303868.5	c.8528G>T	p.Arg2843Leu	missense_variant	Exon 6 of 6	2		ENSP00000368025.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1284370 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 622602

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.85
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.55	T;.
M_CAP	Benign	0.029	D
MetaRNN	Benign	0.11	T;T
MetaSVM	Benign	-0.99	T
PrimateAI	Benign	0.19	T
PROVEAN	Benign	-1.8	N;N
REVEL	Benign	0.078
Sift	Uncertain	0.026	D;D
Sift4G	Uncertain	0.052	T;T
Polyphen		0.093	B;.
Vest4		0.16
MutPred		0.36		Loss of methylation at R2882 (P = 0.06);.;
MVP		0.17
ClinPred		0.13	T
GERP RS		2.5
gMVP		0.093

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-38375666;