rs11958226

Variant names:

• chr5-37491418-C-A
• rs11958226
• NM_018034.4:c.840+11431C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-37491418-C-A
• chr5-37491418-C-G
• chr5-37491418-C-T

Variant summary

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

The NM_018034.4(WDR70):​c.840+11431C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,064 control chromosomes in the GnomAD database, including 28,479 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 0.60 (28479 hom., cov: 32)
• Consequence: WDR70 NM_018034.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509
• Publications: 0 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR70	NM_018034.4	c.840+11431C>A		intron_variant	Intron 8 of 17	ENST00000265107.9	NP_060504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR70	ENST00000265107.9	c.840+11431C>A		intron_variant	Intron 8 of 17	1	NM_018034.4	ENSP00000265107.4
WDR70	ENST00000504564.1	c.840+11431C>A		intron_variant	Intron 8 of 11	1		ENSP00000425841.1
WDR70	ENST00000510699.1	n.197+11431C>A		intron_variant	Intron 2 of 6	5
WDR70	ENST00000511906.5	n.854+11431C>A		intron_variant	Intron 7 of 14	2

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90753 AN: 151946 Hom.: 28454 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.597 AC: 90822 AN: 152064 Hom.: 28479 Cov.: 32 AF XY: 0.597 AC XY: 44407 AN XY: 74358

African (AFR) AF: 0.386 AC: 15997 AN: 41458

American (AMR) AF: 0.673 AC: 10283 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2286 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2699 AN: 5164

South Asian (SAS) AF: 0.689 AC: 3327 AN: 4826

European-Finnish (FIN) AF: 0.673 AC: 7105 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47089 AN: 67986

Other (OTH) AF: 0.588 AC: 1244 AN: 2114

Alfa AF: 0.536 Hom.: 2265

Bravo AF: 0.585

Asia WGS AF: 0.587 AC: 2041 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	4.4
DANN	Benign	0.74
PhyloP100		0.51
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: rs11958226; hg19: chr5-37491520;