6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAAAA

Variant names:

• chr6-169572543-CAAAA-C
• rs376783967
• NM_182552.5:c.2524-7_2524-4delTTTT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182552.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	NM_182552.5	MANE Select	c.2524-7_2524-4delTTTT		splice_region intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+10289_2142+10292delTTTT		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+10289_1950+10292delTTTT		intron	N/A	NP_001337552.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	ENST00000448612.6	TSL:1 MANE Select	c.2524-7_2524-4delTTTT		splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+10289_2142+10292delTTTT		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+10289_533+10292delTTTT		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

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

GnomAD2 exomes AF: 0.00 AC: 0 AN: 10 AF XY: 0.00

Gnomad NFE exome AF: 0.00

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.542 AC: 49837 AN: 91894 Hom.: 12667 Cov.: 0 AF XY: 0.537 AC XY: 22853 AN XY: 42562

African (AFR) AF: 0.269 AC: 4631 AN: 17188

American (AMR) AF: 0.501 AC: 4013 AN: 8008

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 1679 AN: 2768

East Asian (EAS) AF: 0.0286 AC: 62 AN: 2168

South Asian (SAS) AF: 0.472 AC: 1211 AN: 2566

European-Finnish (FIN) AF: 0.679 AC: 2987 AN: 4396

Middle Eastern (MID) AF: 0.583 AC: 112 AN: 192

European-Non Finnish (NFE) AF: 0.646 AC: 34027 AN: 52636

Other (OTH) AF: 0.531 AC: 673 AN: 1268

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.35
Mutation Taster		=98/2	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: rs376783967; hg19: chr6-169972639;