rs2088077

chr5-37556824-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018034.4(WDR70):c.917+40234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,980 control chromosomes in the GnomAD database, including 14,126 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 0.40 (14126 hom., cov: 31)
• Consequence: WDR70 NM_018034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

WDR70 (HGNC:25495): (WD repeat domain 70) Enables enzyme binding activity. Predicted to be involved in regulation of DNA double-strand break processing and regulation of histone H2B conserved C-terminal lysine ubiquitination. Predicted to be active in nucleus and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR70	NM_018034.4	c.917+40234A>G		intron_variant		ENST00000265107.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR70	ENST00000265107.9	c.917+40234A>G		intron_variant		1	NM_018034.4	P1
WDR70	ENST00000504564.1	c.917+40234A>G		intron_variant		1
WDR70	ENST00000510699.1	n.274+40234A>G		intron_variant, non_coding_transcript_variant		5
WDR70	ENST00000511906.5	n.931+40234A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60837 AN: 151862 Hom.: 14124 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.400 AC: 60846 AN: 151980 Hom.: 14126 Cov.: 31 AF XY: 0.399 AC XY: 29657 AN XY: 74270

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.412

Alfa AF: 0.489 Hom.: 24408

Bravo AF: 0.386

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.0
Dann	Benign	0.65

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: rs2088077; hg19: chr5-37556926;