1-27306634-C-T

Variant names:

• chr1-27306634-C-T
• rs3813791
• NM_001276252.2:c.*251C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001276252.2(WDTC1):​c.*251C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDTC1 NM_001276252.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276252.2. 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
	WDTC1	NM_001276252.2	MANE Select	c.*251C>T		3_prime_UTR	Exon 16 of 16	NP_001263181.1
	WDTC1	NM_015023.5		c.*251C>T		3_prime_UTR	Exon 16 of 16	NP_055838.2
	WDTC1	NM_001410767.1		c.*379C>T		3_prime_UTR	Exon 16 of 16	NP_001397696.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDTC1	ENST00000319394.8	TSL:1 MANE Select	c.*251C>T		3_prime_UTR	Exon 16 of 16	ENSP00000317971.3
	WDTC1	ENST00000361771.7	TSL:1	c.*251C>T		3_prime_UTR	Exon 16 of 16	ENSP00000355317.3
	WDTC1	ENST00000472249.2	TSL:5	n.*68-74C>T		intron	N/A	ENSP00000435903.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 394158 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 206654

African (AFR) AF: 0.00 AC: 0 AN: 11400

American (AMR) AF: 0.00 AC: 0 AN: 15948

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12168

East Asian (EAS) AF: 0.00 AC: 0 AN: 26570

South Asian (SAS) AF: 0.00 AC: 0 AN: 41296

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25048

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1720

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 237292

Other (OTH) AF: 0.00 AC: 0 AN: 22716

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.47
PhyloP100		-0.18
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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: rs3813791; hg19: chr1-27633125;