6-169572543-CAAAA-C

Position:

• chr6-169572543-CAAAA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_182552.5(WDR27):​c.2524-7_2524-4delTTTT 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. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (12667 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR27 NM_182552.5 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 6-169572543-CAAAA-C is Benign according to our data. Variant chr6-169572543-CAAAA-C is described in ClinVar as [Benign]. Clinvar id is 2808640.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR27	NM_182552.5	c.2524-7_2524-4delTTTT		splice_region_variant, intron_variant		ENST00000448612.6	NP_872358.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6	c.2524-7_2524-4delTTTT		splice_region_variant, intron_variant		1	NM_182552.5	ENSP00000416289.1
ENSG00000285733	ENST00000648086.1	c.533+10289_533+10292delTTTT		intron_variant				ENSP00000497979.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 49865 AN: 91912 Hom.: 12675 Cov.: 0

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.535

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 AF: 0.542 AC: 49837 AN: 91894 Hom.: 12667 Cov.: 0 AF XY: 0.537 AC XY: 22853 AN XY: 42562

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.531

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 17, 2024

- -

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;