dbSNP rs3760843: DMWD:c.1902+146T>G (chr19-45785448-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004943.2(DMWD):c.1902+146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 8.1e-7 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DMWD
NM_004943.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.887

Publications

15 publications found

Variant links:

Genes affected

DMWD (HGNC:2936): (DM1 locus, WD repeat containing) Predicted to be located in dendrite; nucleus; and perikaryon. [provided by Alliance of Genome Resources, Apr 2022]

DMWD links:

ENSG00000268434 (HGNC:):

ENSG00000268434 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMWD	NM_004943.2 link	c.1902+146T>G		intron_variant	Intron 3 of 4	ENST00000270223.7	NP_004934.1	Q09019Q8WUW6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMWD	ENST00000270223.7 link	c.1902+146T>G		intron_variant	Intron 3 of 4	1	NM_004943.2	ENSP00000270223.5		Q09019
ENSG00000268434	ENST00000595946.1 link	c.120+146T>G		intron_variant	Intron 1 of 3	2		ENSP00000469741.1		M0QYC6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

8.10e-7

AC:

AN:

1233822

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

593934

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26046

American (AMR)

AF:

0.00

AC:

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17874

East Asian (EAS)

AF:

0.00

AC:

AN:

31106

South Asian (SAS)

AF:

0.0000190

AC:

AN:

52498

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29306

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3508

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1006988

Other (OTH)

AF:

0.00

AC:

AN:

51266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

6307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.53

(source)

DANN

Benign

0.16

PhyloP100

-0.89

PromoterAI

-0.0024

Neutral

(source)

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

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rs3760843

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over