rs2243350

chr6-116592949-ATTTTT-Achr6-116592949-ATTTTT-ATTchr6-116592949-ATTTTT-ATTTchr6-116592949-ATTTTT-ATTTTchr6-116592949-ATTTTT-ATTTTTTchr6-116592949-ATTTTT-ATTTTTTTchr6-116592949-ATTTTT-ATTTTTTTT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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]

ACMG classification

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	UniProt
RWDD1	NM_015952.4	c.611-20_611-16del		intron_variant		ENST00000466444.7
RWDD1	NM_001007464.3	c.323-20_323-16del		intron_variant
RWDD1	NM_016104.4	c.323-20_323-16del		intron_variant
RWDD1	XM_047418863.1	c.323-20_323-16del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RWDD1	ENST00000466444.7	c.611-20_611-16del		intron_variant		1	NM_015952.4	P1
RWDD1	ENST00000487832.6	c.323-20_323-16del		intron_variant		1

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

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243350; hg19: chr6-116914112;