rs11084710

Variant names:

• chr19-33161450-G-A
• rs11084710
• NM_173479.4:c.1080+954G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-33161450-G-A
• chr19-33161450-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173479.4(WDR88):​c.1080+954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,904 control chromosomes in the GnomAD database, including 8,644 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 0.32 (8644 hom., cov: 32)
• Consequence: WDR88 NM_173479.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 12 publications found

Genes affected

WDR88 (HGNC:26999): (WD repeat domain 88)

LOC124904691 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR88	NM_173479.4	c.1080+954G>A		intron_variant	Intron 8 of 10	ENST00000355868.4	NP_775750.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR88	ENST00000355868.4	c.1080+954G>A		intron_variant	Intron 8 of 10	2	NM_173479.4	ENSP00000348129.2
WDR88	ENST00000361680.6	c.1080+954G>A		intron_variant	Intron 8 of 11	1		ENSP00000355148.2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47981 AN: 151786 Hom.: 8617 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.316 AC: 48066 AN: 151904 Hom.: 8644 Cov.: 32 AF XY: 0.318 AC XY: 23592 AN XY: 74228

African (AFR) AF: 0.481 AC: 19911 AN: 41418

American (AMR) AF: 0.247 AC: 3768 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2296 AN: 5094

South Asian (SAS) AF: 0.482 AC: 2319 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2347 AN: 10558

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15440 AN: 67994

Other (OTH) AF: 0.305 AC: 639 AN: 2098

Alfa AF: 0.256 Hom.: 10842

Bravo AF: 0.322

Asia WGS AF: 0.477 AC: 1655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.65
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11084710; hg19: chr19-33652356;