19-37884828-CAAAA-CAAA

Variant names:

• chr19-37884828-CA-C
• rs545937452
• NM_001291088.2:c.*103delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001291088.2(WDR87):​c.*103delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 30)
  • Exomes 𝑓: 0.16 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR87 NM_001291088.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

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

LOC105372395 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR87	NM_001291088.2	c.*103delT		3_prime_UTR_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	c.*103delT		3_prime_UTR_variant	Exon 6 of 6	2	NM_001291088.2	ENSP00000405012.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 243 AN: 115908 Hom.: 0 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.00108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00161

Gnomad ASJ AF: 0.00249

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.000274

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.00196

GnomAD4 exome AF: 0.160 AC: 112738 AN: 703424 Hom.: 0 Cov.: 0 AF XY: 0.161 AC XY: 53914 AN XY: 334986

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.172

Gnomad4 ASJ exome AF: 0.179

Gnomad4 EAS exome AF: 0.157

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00210 AC: 244 AN: 115926 Hom.: 0 Cov.: 30 AF XY: 0.00238 AC XY: 131 AN XY: 55112

Gnomad4 AFR AF: 0.00111

Gnomad4 AMR AF: 0.00161

Gnomad4 ASJ AF: 0.00249

Gnomad4 EAS AF: 0.00119

Gnomad4 SAS AF: 0.000276

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.00169

Gnomad4 OTH AF: 0.00195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs545937452; hg19: chr19-38375468;