chr6-169572543-CAAA-C

Variant names:

• chr6-169572543-CAAA-C
• rs376783967
• NM_182552.5:c.2524-6_2524-4delTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_182552.5(WDR27):​c.2524-6_2524-4delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0046 (4 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR27 NM_182552.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

WDR27 (HGNC:21248): (WD repeat domain 27) This gene encodes a protein with multiple WD repeats. Proteins with these repeats may form scaffolds for protein-protein interaction and play key roles in cell signalling. Alternative splicing results in multiple transcript variants, but the full-length structure of some of these variants cannot be determined. [provided by RefSeq, Nov 2015]

ENSG00000285733 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR27	NM_182552.5	c.2524-6_2524-4delTTT		splice_region_variant, intron_variant	Intron 24 of 25	ENST00000448612.6	NP_872358.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6	c.2524-6_2524-4delTTT		splice_region_variant, intron_variant	Intron 24 of 25	1	NM_182552.5	ENSP00000416289.1
ENSG00000285733	ENST00000648086.1	c.533+10290_533+10292delTTT		intron_variant	Intron 5 of 7			ENSP00000497979.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 429 AN: 92288 Hom.: 4 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.00141

Gnomad AMR AF: 0.00299

Gnomad ASJ AF: 0.00252

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00153

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00980

Gnomad NFE AF: 0.00191

Gnomad OTH AF: 0.00474

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 28 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00465 AC: 429 AN: 92270 Hom.: 4 Cov.: 0 AF XY: 0.00440 AC XY: 188 AN XY: 42706

Gnomad4 AFR AF: 0.0161

Gnomad4 AMR AF: 0.00299

Gnomad4 ASJ AF: 0.00252

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00154

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00191

Gnomad4 OTH AF: 0.00472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs376783967; hg19: chr6-169972639;