dbSNP rs56151250: UEVLD:p.Val408Val (chr11-18534354-C-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001040697.4(UEVLD):c.1224G>C(p.Val408Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,540,612 control chromosomes in the GnomAD database, including 27,323 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 0.16 ( 2581 hom., cov: 32)

Exomes 𝑓: 0.17 ( 24742 hom. )

Consequence

UEVLD
NM_001040697.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

9 publications found

Variant links:

Genes affected

UEVLD (HGNC:30866): (UEV and lactate/malate dehyrogenase domains) Predicted to enable oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. Predicted to be involved in several processes, including carbohydrate metabolic process; cellular protein modification process; and protein transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

UEVLD links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=-0.535 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UEVLD	NM_001040697.4 link	c.1224G>C	p.Val408Val	synonymous_variant	Exon 11 of 12	ENST00000396197.8	NP_001035787.1	Q8IX04-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UEVLD	ENST00000396197.8 link	c.1224G>C	p.Val408Val	synonymous_variant	Exon 11 of 12	5	NM_001040697.4	ENSP00000379500.2		Q8IX04-1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24405

AN:

152014

Hom.:

2560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0693

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.175

GnomAD2 exomes

AF:

0.197

AC:

38804

AN:

196938

AF XY:

0.199

show subpopulations

Gnomad AFR exome

AF:

0.0604

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.121

Gnomad EAS exome

AF:

0.374

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.175

AC:

242923

AN:

1388480

Hom.:

24742

Cov.:

AF XY:

0.177

AC XY:

122419

AN XY:

689726

show subpopulations

African (AFR)

AF:

0.0616

AC:

1833

AN:

29744

American (AMR)

AF:

0.222

AC:

6712

AN:

30202

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

3194

AN:

24658

East Asian (EAS)

AF:

0.446

AC:

15459

AN:

34646

South Asian (SAS)

AF:

0.297

AC:

21649

AN:

72960

European-Finnish (FIN)

AF:

0.293

AC:

15409

AN:

52590

Middle Eastern (MID)

AF:

0.162

AC:

909

AN:

5600

European-Non Finnish (NFE)

AF:

0.155

AC:

167243

AN:

1080556

Other (OTH)

AF:

0.183

AC:

10515

AN:

57524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.420

Heterozygous variant carriers

8624

17247

25871

34494

43118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6172

12344

18516

24688

30860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.161

AC:

24449

AN:

152132

Hom.:

2581

Cov.:

AF XY:

0.173

AC XY:

12852

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0697

AC:

2896

AN:

41542

American (AMR)

AF:

0.184

AC:

2813

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

456

AN:

3466

East Asian (EAS)

AF:

0.412

AC:

2128

AN:

5164

South Asian (SAS)

AF:

0.332

AC:

1599

AN:

4822

European-Finnish (FIN)

AF:

0.312

AC:

3294

AN:

10546

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10739

AN:

68000

Other (OTH)

AF:

0.183

AC:

387

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1011

2022

3034

4045

5056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.155

Hom.:

694

Bravo

AF:

0.148

Asia WGS

AF:

0.405

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

3.0

(source)

DANN

Benign

0.75

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over