6-116592949-ATTTTT-ATTTTTT

Position:

• chr6-116592949-ATTTTT-ATTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000466444.7(RWDD1):​c.611-16dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,376,506 control chromosomes in the GnomAD database, including 1,124 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1027 hom., cov: 29)
  • Exomes 𝑓: 0.13 (97 hom.)
• Consequence: RWDD1 ENST00000466444.7 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RWDD1	NM_015952.4	c.611-16dupT		intron_variant		ENST00000466444.7	NP_057036.2
RWDD1	NM_001007464.3	c.323-16dupT		intron_variant			NP_001007465.1
RWDD1	NM_016104.4	c.323-16dupT		intron_variant			NP_057188.2
RWDD1	XM_047418863.1	c.323-16dupT		intron_variant			XP_047274819.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 16485 AN: 141908 Hom.: 1024 Cov.: 29

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0244

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.0604

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.130 AC: 160058 AN: 1234554 Hom.: 97 Cov.: 0 AF XY: 0.127 AC XY: 78284 AN XY: 617278

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.202

Gnomad4 ASJ exome AF: 0.124

Gnomad4 EAS exome AF: 0.0688

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0900

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.129

GnomAD4 genome AF: 0.116 AC: 16501 AN: 141952 Hom.: 1027 Cov.: 29 AF XY: 0.115 AC XY: 7899 AN XY: 68802

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.0735

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs2243350; hg19: chr6-116914112;