chr7-151379575-G-C

Variant names:

• chr7-151379575-G-C
• rs11764733
• XM_011516144.4:c.*698C>G

Variant summary

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

The XM_011516144.4(WDR86):​c.*698C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,038 control chromosomes in the GnomAD database, including 18,349 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 0.47 (18349 hom., cov: 32)
• Consequence: WDR86 XM_011516144.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 3 publications found

Genes affected

WDR86 (HGNC:28020): (WD repeat domain 86)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463000.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR86	ENST00000463000.1	TSL:2	n.143-2428C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71672 AN: 151920 Hom.: 18311 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.472 AC: 71753 AN: 152038 Hom.: 18349 Cov.: 32 AF XY: 0.470 AC XY: 34939 AN XY: 74322

African (AFR) AF: 0.683 AC: 28318 AN: 41480

American (AMR) AF: 0.383 AC: 5848 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5178

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4816

European-Finnish (FIN) AF: 0.426 AC: 4494 AN: 10538

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27727 AN: 67960

Other (OTH) AF: 0.434 AC: 918 AN: 2116

Alfa AF: 0.324 Hom.: 981

Bravo AF: 0.471

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11764733; hg19: chr7-151076661; COSMIC: COSV57839574;