Variant 6-83193907-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_033411.5(RWDD2A):c.-140-405G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 153,298 control chromosomes in the GnomAD database, including 7,287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 7257 hom., cov: 31)

Exomes 𝑓: 0.18 ( 30 hom. )

Consequence

RWDD2A
NM_033411.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.219

Variant links:

Genes affected

RWDD2A (HGNC:21385): (RWD domain containing 2A)

RWDD2A links:

PGM3 (HGNC:8907): (phosphoglucomutase 3) This gene encodes a member of the phosphohexose mutase family. The encoded protein mediates both glycogen formation and utilization by catalyzing the interconversion of glucose-1-phosphate and glucose-6-phosphate. A non-synonymous single nucleotide polymorphism in this gene may play a role in resistance to diabetic nephropathy and neuropathy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

PGM3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 6-83193907-G-C is Benign according to our data. Variant chr6-83193907-G-C is described in ClinVar as [Benign]. Clinvar id is 1222964.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RWDD2A	NM_033411.5 linkuse as main transcript	c.-140-405G>C		intron_variant		ENST00000369724.5	NP_219479.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RWDD2A	ENST00000369724.5 linkuse as main transcript	c.-140-405G>C	intron_variant		1	NM_033411.5	ENSP00000358739	P1	Q9UIY3-1
PGM3	ENST00000506587.5 linkuse as main transcript	c.-140C>G	5_prime_UTR_variant	1/14	2		ENSP00000425809		O95394-4
PGM3	ENST00000507554.2 linkuse as main transcript	c.-87C>G	5_prime_UTR_variant	1/13	4		ENSP00000425558	P1	O95394-1

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

43988

AN:

151504

Hom.:

7235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.0773

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.298

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.263

GnomAD4 exome

AF:

0.179

AC:

299

AN:

1674

Hom.:

Cov.:

AF XY:

0.193

AC XY:

195

AN XY:

1012

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.136

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.291

AC:

44057

AN:

151624

Hom.:

7257

Cov.:

AF XY:

0.290

AC XY:

21502

AN XY:

74062

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.218

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.298

Gnomad4 NFE

AF:

0.233

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.263

Hom.:

783

Bravo

AF:

0.292

Asia WGS

AF:

0.212

AC:

740

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 28, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.3

DANN

Benign

0.47

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over