chr19-37884828-C-CA

Position:

• chr19-37884828-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001291088.2(WDR87):​c.*103_*104insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 846,348 control chromosomes in the GnomAD database, including 379 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.077 (322 hom., cov: 30)
  • Exomes 𝑓: 0.15 (57 hom.)
• Consequence: WDR87 NM_001291088.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.332

Genes affected

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

LOC105372395 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-37884828-C-CA is Benign according to our data. Variant chr19-37884828-C-CA is described in ClinVar as [Benign]. Clinvar id is 1260155.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR87	NM_001291088.2	c.*103_*104insT		3_prime_UTR_variant	6/6	ENST00000447313.7
LOC105372395	XR_935962.3	n.621+343dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR87	ENST00000447313.7	c.*103_*104insT		3_prime_UTR_variant	6/6	2	NM_001291088.2	A2

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 8960 AN: 115910 Hom.: 320 Cov.: 30

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00289

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0388

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0634

GnomAD4 exome AF: 0.155 AC: 112926 AN: 730418 Hom.: 57 Cov.: 0 AF XY: 0.156 AC XY: 54221 AN XY: 348094

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0773 AC: 8963 AN: 115930 Hom.: 322 Cov.: 30 AF XY: 0.0768 AC XY: 4234 AN XY: 55122

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0983

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0502

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0636

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 16, 2019

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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;