19-37884828-CAAAA-CA

Variant names:

• chr19-37884828-CAAA-C
• rs545937452
• ENST00000447313:c.*101_*103delTTT

Variant summary

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

The NM_001291088.2(WDR87):​c.*101_*103delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000682 in 879,284 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00078 (0 hom.)
• 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR87	NM_001291088.2	c.*101_*103delTTT		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.*101_*103delTTT		3_prime_UTR_variant	Exon 6 of 6	2	NM_001291088.2	ENSP00000405012.2

Frequencies

GnomAD3 genomes AF: 0.0000258 AC: 3 AN: 116056 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000636

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000161

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000782 AC: 597 AN: 763228 Hom.: 0 AF XY: 0.000801 AC XY: 292 AN XY: 364506

Gnomad4 AFR exome AF: 0.000548

Gnomad4 AMR exome AF: 0.00104

Gnomad4 ASJ exome AF: 0.000525

Gnomad4 EAS exome AF: 0.000219

Gnomad4 SAS exome AF: 0.000774

Gnomad4 FIN exome AF: 0.000261

Gnomad4 NFE exome AF: 0.000841

Gnomad4 OTH exome AF: 0.000594

GnomAD4 genome AF: 0.0000258 AC: 3 AN: 116056 Hom.: 0 Cov.: 30 AF XY: 0.0000181 AC XY: 1 AN XY: 55154

Gnomad4 AFR AF: 0.0000636

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000161

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;