11-18570024-A-G

Variant names:

• chr11-18570024-A-G
• rs11024717
• NM_001040697.4:c.357+190T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 8 publications found

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UEVLD	NM_001040697.4	c.357+190T>C		intron_variant	Intron 4 of 11	ENST00000396197.8	NP_001035787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UEVLD	ENST00000396197.8	c.357+190T>C		intron_variant	Intron 4 of 11	5	NM_001040697.4	ENSP00000379500.2

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51024 AN: 151976 Hom.: 10375 Cov.: 32

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

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

GnomAD4 genome AF: 0.335 AC: 51017 AN: 152094 Hom.: 10378 Cov.: 32 AF XY: 0.334 AC XY: 24805 AN XY: 74346

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.62
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11024717; hg19: chr11-18591571;