GeneBe

rs2243350

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015952.4(RWDD1):​c.611-20_611-16del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000077 in 1,299,040 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: not found (cov: 29)
Exomes 𝑓: 7.7e-7 ( 0 hom. )

Consequence

RWDD1
NM_015952.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RWDD1NM_015952.4 linkuse as main transcriptc.611-20_611-16del intron_variant ENST00000466444.7 NP_057036.2
RWDD1NM_001007464.3 linkuse as main transcriptc.323-20_323-16del intron_variant NP_001007465.1
RWDD1NM_016104.4 linkuse as main transcriptc.323-20_323-16del intron_variant NP_057188.2
RWDD1XM_047418863.1 linkuse as main transcriptc.323-20_323-16del intron_variant XP_047274819.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RWDD1ENST00000466444.7 linkuse as main transcriptc.611-20_611-16del intron_variant 1 NM_015952.4 ENSP00000420357 P1Q9H446-1
RWDD1ENST00000487832.6 linkuse as main transcriptc.323-20_323-16del intron_variant 1 ENSP00000428778 Q9H446-2

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
7.70e-7
AC:
1
AN:
1299040
Hom.:
0
AF XY:
0.00000154
AC XY:
1
AN XY:
648682
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000100
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2243350; hg19: chr6-116914112; API