7-151379575-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR86	XM_011516144.4	c.*698C>G		3_prime_UTR_variant	Exon 7 of 7		XP_011514446.1
WDR86	XM_011516145.4	c.*698C>G		3_prime_UTR_variant	Exon 6 of 6		XP_011514447.1
WDR86	XM_011516147.4	c.*798C>G		3_prime_UTR_variant	Exon 6 of 6		XP_011514449.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR86	ENST00000463000.1	n.143-2428C>G		intron_variant	Intron 1 of 1	2

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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.434

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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