chr19-37834896-C-G

Position:

• chr19-37834896-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592640.5(WDR87BP):​n.281-1382G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,594 control chromosomes in the GnomAD database, including 4,694 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 0.25 (4694 hom., cov: 30)
• Consequence: WDR87BP ENST00000592640.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

WDR87BP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR87BP	NR_040015.1	n.281-1382G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR87BP	ENST00000592640.5	n.281-1382G>C		intron_variant		1
WDR87BP	ENST00000433142.6	n.356-1382G>C		intron_variant		3
WDR87BP	ENST00000587395.5	n.502-1382G>C		intron_variant		4
WDR87BP	ENST00000636341.1	n.73-1382G>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37584 AN: 151474 Hom.: 4686 Cov.: 30

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.248 AC: 37615 AN: 151594 Hom.: 4694 Cov.: 30 AF XY: 0.252 AC XY: 18655 AN XY: 74074

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.260

Alfa AF: 0.210 Hom.: 1917

Bravo AF: 0.255

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16975963; hg19: chr19-38325536; COSMIC: COSV70465428;