Genetic Variant UEVLD:c.357+190T>C (chr11-18570024-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040697.4(UEVLD):c.357+190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 509,320 control chromosomes in the GnomAD database, including 43,639 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 0.34 ( 10378 hom., cov: 32)

Exomes 𝑓: 0.42 ( 33261 hom. )

Consequence

UEVLD
NM_001040697.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46

Publications

8 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040697.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UEVLD	NM_001040697.4	MANE Select	c.357+190T>C	intron	N/A	NP_001035787.1
UEVLD	NM_001261382.3		c.291+190T>C	intron	N/A	NP_001248311.1
UEVLD	NM_018314.6		c.357+190T>C	intron	N/A	NP_060784.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UEVLD	ENST00000396197.8	TSL:5 MANE Select	c.357+190T>C	intron	N/A	ENSP00000379500.2
UEVLD	ENST00000543987.5	TSL:1	c.357+190T>C	intron	N/A	ENSP00000442974.1
UEVLD	ENST00000320750.10	TSL:1	c.291+190T>C	intron	N/A	ENSP00000323353.6

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51024

AN:

151976

Hom.:

10375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0956

Gnomad AMI

AF:

0.505

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.368

GnomAD4 exome

AF:

0.420

AC:

149905

AN:

357226

Hom.:

33261

Cov.:

AF XY:

0.416

AC XY:

77809

AN XY:

187028

show subpopulations

African (AFR)

AF:

0.0979

AC:

757

AN:

7736

American (AMR)

AF:

0.356

AC:

3285

AN:

9238

Ashkenazi Jewish (ASJ)

AF:

0.436

AC:

4268

AN:

9784

East Asian (EAS)

AF:

0.239

AC:

4441

AN:

18596

South Asian (SAS)

AF:

0.327

AC:

10384

AN:

31754

European-Finnish (FIN)

AF:

0.364

AC:

6427

AN:

17636

Middle Eastern (MID)

AF:

0.436

AC:

631

AN:

1448

European-Non Finnish (NFE)

AF:

0.464

AC:

111940

AN:

241434

Other (OTH)

AF:

0.397

AC:

7772

AN:

19600

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4052

8103

12155

16206

20258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1378

2756

4134

5512

6890

<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:

0.335

AC:

51017

AN:

152094

Hom.:

10378

Cov.:

AF XY:

0.334

AC XY:

24805

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.0953

AC:

3957

AN:

41538

American (AMR)

AF:

0.390

AC:

5949

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

1459

AN:

3468

East Asian (EAS)

AF:

0.261

AC:

1349

AN:

5172

South Asian (SAS)

AF:

0.320

AC:

1541

AN:

4818

European-Finnish (FIN)

AF:

0.374

AC:

3944

AN:

10554

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.463

AC:

31462

AN:

67966

Other (OTH)

AF:

0.364

AC:

768

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1541

3082

4623

6164

7705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<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:

0.362

Hom.:

4058

Bravo

AF:

0.323

Asia WGS

AF:

0.253

AC:

881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.1

(source)

DANN

Benign

0.62

PhyloP100

1.5

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over