rs16975963

Variant names:

• chr19-37834896-C-G
• rs16975963
• ENST00000592640.6:n.303-1382G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-37834896-C-G
• chr19-37834896-C-T

Variant summary

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

The ENST00000592640.6(WDR87BP):​n.303-1382G>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 ENST00000592640.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 17 publications found

Genes affected

WDR87BP (HGNC:):

WDR87BP (HGNC:55125): (WD repeat domain 87B, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592640.6. 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
	WDR87BP	NR_040015.1		n.281-1382G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR87BP	ENST00000592640.6	TSL:1	n.303-1382G>C		intron	N/A
	WDR87BP	ENST00000433142.6	TSL:3	n.356-1382G>C		intron	N/A
	WDR87BP	ENST00000587395.6	TSL:4	n.502-1382G>C		intron	N/A

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

African (AFR) AF: 0.276 AC: 11427 AN: 41330

American (AMR) AF: 0.284 AC: 4314 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 976 AN: 3462

East Asian (EAS) AF: 0.288 AC: 1476 AN: 5126

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4796

European-Finnish (FIN) AF: 0.262 AC: 2744 AN: 10458

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14653 AN: 67896

Other (OTH) AF: 0.260 AC: 547 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		-0.23

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: rs16975963;

hg19: chr19-38325536;

COSMIC: COSV70465428;