11-18570024-A-G

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UEVLDNM_001040697.4 linkc.357+190T>C intron_variant ENST00000396197.8 NP_001035787.1 Q8IX04-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UEVLDENST00000396197.8 linkc.357+190T>C intron_variant 5 NM_001040697.4 ENSP00000379500.2 Q8IX04-1

Frequencies

GnomAD3 genomes
AF:
0.336
AC:
51024
AN:
151976
Hom.:
10375
Cov.:
32
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.:
6
AF XY:
0.416
AC XY:
77809
AN XY:
187028
show subpopulations
Gnomad4 AFR exome
AF:
0.0979
Gnomad4 AMR exome
AF:
0.356
Gnomad4 ASJ exome
AF:
0.436
Gnomad4 EAS exome
AF:
0.239
Gnomad4 SAS exome
AF:
0.327
Gnomad4 FIN exome
AF:
0.364
Gnomad4 NFE exome
AF:
0.464
Gnomad4 OTH exome
AF:
0.397
GnomAD4 genome
AF:
0.335
AC:
51017
AN:
152094
Hom.:
10378
Cov.:
32
AF XY:
0.334
AC XY:
24805
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.0953
Gnomad4 AMR
AF:
0.390
Gnomad4 ASJ
AF:
0.421
Gnomad4 EAS
AF:
0.261
Gnomad4 SAS
AF:
0.320
Gnomad4 FIN
AF:
0.374
Gnomad4 NFE
AF:
0.463
Gnomad4 OTH
AF:
0.364
Alfa
AF:
0.338
Hom.:
1958
Bravo
AF:
0.323
Asia WGS
AF:
0.253
AC:
881
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
8.1
DANN
Benign
0.62

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.

Other links and lift over

dbSNP: rs11024717; hg19: chr11-18591571; API