rs1983721

Positions:

• chr6-116584324-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015952.4(RWDD1):​c.140-403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,074 control chromosomes in the GnomAD database, including 13,469 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13469 hom., cov: 33)
• Consequence: RWDD1 NM_015952.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RWDD1	NM_015952.4	c.140-403A>G		intron_variant		ENST00000466444.7	NP_057036.2
RWDD1	NM_001007464.3	c.-149-403A>G		intron_variant			NP_001007465.1
RWDD1	NM_016104.4	c.-149-403A>G		intron_variant			NP_057188.2
RWDD1	XM_047418863.1	c.-149-403A>G		intron_variant			XP_047274819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RWDD1	ENST00000466444.7	c.140-403A>G		intron_variant		1	NM_015952.4	ENSP00000420357.2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63480 AN: 151956 Hom.: 13473 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.418 AC: 63491 AN: 152074 Hom.: 13469 Cov.: 33 AF XY: 0.418 AC XY: 31035 AN XY: 74326

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.438

Alfa AF: 0.444 Hom.: 25468

Bravo AF: 0.417

Asia WGS AF: 0.432 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.75

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: rs1983721; hg19: chr6-116905487; COSMIC: COSV63972953;