6-116592949-ATTTTT-ATTTTTTT

Position:

• chr6-116592949-ATTTTT-ATTTTTTT

Variant summary

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

The NM_015952.4(RWDD1):​c.611-17_611-16dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00127 in 1,437,516 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 0.00081 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0013 (0 hom.)
• Consequence: RWDD1 NM_015952.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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	Protein	UniProt
RWDD1	NM_015952.4	c.611-17_611-16dupTT		intron_variant		ENST00000466444.7	NP_057036.2
RWDD1	NM_001007464.3	c.323-17_323-16dupTT		intron_variant			NP_001007465.1
RWDD1	NM_016104.4	c.323-17_323-16dupTT		intron_variant			NP_057188.2
RWDD1	XM_047418863.1	c.323-17_323-16dupTT		intron_variant			XP_047274819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RWDD1	ENST00000466444.7	c.611-17_611-16dupTT		intron_variant		1	NM_015952.4	ENSP00000420357.2
RWDD1	ENST00000487832.6	c.323-17_323-16dupTT		intron_variant		1		ENSP00000428778.1

Frequencies

GnomAD3 genomes AF: 0.000782 AC: 111 AN: 142010 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000281

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000450

Gnomad FIN AF: 0.000115

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000139

Gnomad OTH AF: 0.000515

GnomAD4 exome AF: 0.00132 AC: 1708 AN: 1295458 Hom.: 0 Cov.: 0 AF XY: 0.00130 AC XY: 844 AN XY: 646878

Gnomad4 AFR exome AF: 0.00463

Gnomad4 AMR exome AF: 0.00551

Gnomad4 ASJ exome AF: 0.00161

Gnomad4 EAS exome AF: 0.000493

Gnomad4 SAS exome AF: 0.00157

Gnomad4 FIN exome AF: 0.00146

Gnomad4 NFE exome AF: 0.00107

Gnomad4 OTH exome AF: 0.00138

GnomAD4 genome AF: 0.000810 AC: 115 AN: 142058 Hom.: 0 Cov.: 29 AF XY: 0.000741 AC XY: 51 AN XY: 68862

Gnomad4 AFR AF: 0.00252

Gnomad4 AMR AF: 0.000281

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000452

Gnomad4 FIN AF: 0.000115

Gnomad4 NFE AF: 0.000139

Gnomad4 OTH AF: 0.000512

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;