19-37884828-CAAAA-CAAAAAA

Variant names:

• chr19-37884828-C-CAA
• rs545937452
• NM_001291088.2:c.*102_*103dupTT

Variant summary

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

The NM_001291088.2(WDR87):​c.*102_*103dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 877,844 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 0.00027 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0030 (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.*102_*103dupTT		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.*102_*103dupTT		3_prime_UTR_variant	Exon 6 of 6	2	NM_001291088.2	ENSP00000405012.2

Frequencies

GnomAD3 genomes AF: 0.000267 AC: 31 AN: 116068 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000159

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00107

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000237

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000323

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000204

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00304 AC: 2313 AN: 761756 Hom.: 0 Cov.: 0 AF XY: 0.00294 AC XY: 1068 AN XY: 363724

Gnomad4 AFR exome AF: 0.00391

Gnomad4 AMR exome AF: 0.00339

Gnomad4 ASJ exome AF: 0.00123

Gnomad4 EAS exome AF: 0.00343

Gnomad4 SAS exome AF: 0.00310

Gnomad4 FIN exome AF: 0.00241

Gnomad4 NFE exome AF: 0.00303

Gnomad4 OTH exome AF: 0.00367

GnomAD4 genome AF: 0.000267 AC: 31 AN: 116088 Hom.: 0 Cov.: 30 AF XY: 0.000362 AC XY: 20 AN XY: 55198

Gnomad4 AFR AF: 0.000159

Gnomad4 AMR AF: 0.00107

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000238

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000323

Gnomad4 NFE AF: 0.000204

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;