Genetic Variant RWDD1:c.611-16delT (chr6-116592949-AT-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015952.4(RWDD1):c.611-16delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0046 in 141,680 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0046 ( 1 hom., cov: 29)

Exomes 𝑓: 0.26 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RWDD1
NM_015952.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

Publications

2 publications found

Variant links:

Genes affected

RWDD1 (HGNC:20993): (RWD domain containing 1) Predicted to be involved in several processes, including cellular response to lipid; cytoplasmic translation; and positive regulation of androgen receptor activity. Predicted to be located in cytoplasm. Predicted to be part of polysome. [provided by Alliance of Genome Resources, Apr 2022]

RWDD1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015952.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RWDD1	NM_015952.4	MANE Select	c.611-16delT	intron	N/A	NP_057036.2	Q9H446-1
RWDD1	NM_001007464.3		c.323-16delT	intron	N/A	NP_001007465.1	Q9H446-2
RWDD1	NM_016104.4		c.323-16delT	intron	N/A	NP_057188.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RWDD1	ENST00000466444.7	TSL:1 MANE Select	c.611-30delT		intron	N/A	ENSP00000420357.2	Q9H446-1
	RWDD1	ENST00000487832.6	TSL:1	c.323-30delT		intron	N/A	ENSP00000428778.1	Q9H446-2

Frequencies

GnomAD3 genomes

AF:

0.00447

AC:

633

AN:

141636

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00344

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00269

Gnomad EAS

AF:

0.00350

Gnomad SAS

AF:

0.00113

Gnomad FIN

AF:

0.0201

Gnomad MID

AF:

0.00336

Gnomad NFE

AF:

0.00385

Gnomad OTH

AF:

0.00516

GnomAD2 exomes

AF:

0.346

AC:

50424

AN:

145910

AF XY:

0.350

show subpopulations

Gnomad AFR exome

AF:

0.302

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.358

Gnomad EAS exome

AF:

0.402

Gnomad FIN exome

AF:

0.375

Gnomad NFE exome

AF:

0.356

Gnomad OTH exome

AF:

0.357

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.263

AC:

274497

AN:

1041750

Hom.:

Cov.:

AF XY:

0.268

AC XY:

139459

AN XY:

521206

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.227

AC:

5550

AN:

24396

American (AMR)

AF:

0.210

AC:

6791

AN:

32394

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

5427

AN:

19582

East Asian (EAS)

AF:

0.342

AC:

10168

AN:

29696

South Asian (SAS)

AF:

0.290

AC:

18342

AN:

63258

European-Finnish (FIN)

AF:

0.291

AC:

11126

AN:

38272

Middle Eastern (MID)

AF:

0.272

AC:

1091

AN:

4018

European-Non Finnish (NFE)

AF:

0.260

AC:

204211

AN:

786422

Other (OTH)

AF:

0.270

AC:

11791

AN:

43712

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.277

Heterozygous variant carriers

24820

49640

74461

99281

124101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

7210

14420

21630

28840

36050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00460

AC:

652

AN:

141680

Hom.:

Cov.:

AF XY:

0.00527

AC XY:

362

AN XY:

68640

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00384

AC:

149

AN:

38794

American (AMR)

AF:

0.00274

AC:

AN:

14210

Ashkenazi Jewish (ASJ)

AF:

0.00269

AC:

AN:

3340

East Asian (EAS)

AF:

0.00351

AC:

AN:

4848

South Asian (SAS)

AF:

0.00136

AC:

AN:

4418

European-Finnish (FIN)

AF:

0.0201

AC:

172

AN:

8568

Middle Eastern (MID)

AF:

0.00362

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00385

AC:

248

AN:

64416

Other (OTH)

AF:

0.00565

AC:

AN:

1948

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.337

Heterozygous variant carriers

125

166

208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0873

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.068

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

6-116592949-ATTTTT-ATTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over