Genetic Variant RWDD1:c.611-18_611-16delTTT (chr6-116592949-ATTT-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.611-18_611-16delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,294,562 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 29)

Exomes 𝑓: 0.00013 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RWDD1
NM_015952.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.810

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.611-18_611-16delTTT	intron	N/A	NP_057036.2	Q9H446-1
RWDD1	NM_001007464.3		c.323-18_323-16delTTT	intron	N/A	NP_001007465.1	Q9H446-2
RWDD1	NM_016104.4		c.323-18_323-16delTTT	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.611-30_611-28delTTT		intron	N/A	ENSP00000420357.2	Q9H446-1
	RWDD1	ENST00000487832.6	TSL:1	c.323-30_323-28delTTT		intron	N/A	ENSP00000428778.1	Q9H446-2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

141990

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000535

AC:

AN:

145910

AF XY:

0.000603

show subpopulations

Gnomad AFR exome

AF:

0.0000945

Gnomad AMR exome

AF:

0.000618

Gnomad ASJ exome

AF:

0.00108

Gnomad EAS exome

AF:

0.000643

Gnomad FIN exome

AF:

0.000733

Gnomad NFE exome

AF:

0.000463

Gnomad OTH exome

AF:

0.00116

GnomAD4 exome

AF:

0.000132

AC:

171

AN:

1294562

Hom.:

AF XY:

0.000147

AC XY:

AN XY:

646474

show subpopulations

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

African (AFR)

AF:

0.000104

AC:

AN:

28952

American (AMR)

AF:

0.000310

AC:

AN:

35444

Ashkenazi Jewish (ASJ)

AF:

0.000349

AC:

AN:

22936

East Asian (EAS)

AF:

0.000165

AC:

AN:

36472

South Asian (SAS)

AF:

0.000200

AC:

AN:

75034

European-Finnish (FIN)

AF:

0.000520

AC:

AN:

44268

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4802

European-Non Finnish (NFE)

AF:

0.0000977

AC:

AN:

992896

Other (OTH)

AF:

0.000149

AC:

AN:

53758

⚠️ 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: 0.240

Heterozygous variant carriers

112

140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

141990

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

68786

African (AFR)

AF:

0.00

AC:

AN:

38740

American (AMR)

AF:

0.00

AC:

AN:

14222

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3342

East Asian (EAS)

AF:

0.00

AC:

AN:

4872

South Asian (SAS)

AF:

0.00

AC:

AN:

4440

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8668

Middle Eastern (MID)

AF:

0.00

AC:

AN:

298

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64604

Other (OTH)

AF:

0.00

AC:

AN:

1942

Alfa

AF:

0.00102

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.81

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-ATT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over