rs17750684

Positions:

• chr14-63629744-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_080666.4(WDR89):​c.-137-4711G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 152,262 control chromosomes in the GnomAD database, including 33 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 0.018 (33 hom., cov: 32)
• Consequence: WDR89 NM_080666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

Genes affected

WDR89 (HGNC:20489): (WD repeat domain 89)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0178 (2707/152262) while in subpopulation NFE AF= 0.0271 (1843/68026). AF 95% confidence interval is 0.0261. There are 33 homozygotes in gnomad4. There are 1356 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR89	NM_080666.4	c.-137-4711G>A		intron_variant		ENST00000620954.2	NP_542397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR89	ENST00000620954.2	c.-137-4711G>A		intron_variant		6	NM_080666.4	ENSP00000480112.1
WDR89	ENST00000267522.7	c.-137-4711G>A		intron_variant		1		ENSP00000267522.3
WDR89	ENST00000394942.2	c.-32+12060G>A		intron_variant		5		ENSP00000378399.2
WDR89	ENST00000554717.1	c.-137-4711G>A		intron_variant		2		ENSP00000451702.1

Frequencies

GnomAD3 genomes AF: 0.0178 AC: 2707 AN: 152144 Hom.: 33 Cov.: 32

Gnomad AFR AF: 0.00468

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00622

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0124

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0178 AC: 2707 AN: 152262 Hom.: 33 Cov.: 32 AF XY: 0.0182 AC XY: 1356 AN XY: 74452

Gnomad4 AFR AF: 0.00467

Gnomad4 AMR AF: 0.0166

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0303

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.0225 Hom.: 7

Bravo AF: 0.0158

Asia WGS AF: 0.00318 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17750684; hg19: chr14-64096462;