rs3813790

Variant names:

• chr1-27296637-G-A
• rs3813790
• NM_001276252.2:c.949+236G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-27296637-G-A
• chr1-27296637-G-C

Variant summary

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

The NM_001276252.2(WDTC1):​c.949+236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,024 control chromosomes in the GnomAD database, including 41,869 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 0.73 (41869 hom., cov: 31)
• Consequence: WDTC1 NM_001276252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

WDTC1 (HGNC:29175): (WD and tetratricopeptide repeats 1) Predicted to enable enzyme inhibitor activity; histone binding activity; and histone deacetylase binding activity. Predicted to be involved in negative regulation of fatty acid biosynthetic process. Predicted to act upstream of or within several processes, including cellular response to insulin stimulus; glucose metabolic process; and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in cytoplasm. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDTC1	NM_001276252.2	c.949+236G>A		intron_variant	Intron 10 of 15	ENST00000319394.8	NP_001263181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDTC1	ENST00000319394.8	c.949+236G>A		intron_variant	Intron 10 of 15	1	NM_001276252.2	ENSP00000317971.3
WDTC1	ENST00000361771.7	c.949+236G>A		intron_variant	Intron 10 of 15	1		ENSP00000355317.3
WDTC1	ENST00000447062.2	n.949+236G>A		intron_variant	Intron 9 of 15	2		ENSP00000434578.1
WDTC1	ENST00000491239.2	n.623+236G>A		intron_variant	Intron 5 of 9	2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111192 AN: 151906 Hom.: 41849 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.732 AC: 111247 AN: 152024 Hom.: 41869 Cov.: 31 AF XY: 0.732 AC XY: 54380 AN XY: 74310

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.754

Alfa AF: 0.756 Hom.: 6467

Bravo AF: 0.727

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.8
DANN	Benign	0.51

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: rs3813790; hg19: chr1-27623128;