rs11024717

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-18570024-A-C
• chr11-18570024-A-G
• chr11-18570024-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040697.4(UEVLD):​c.357+190T>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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: 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=-0.83).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 358618 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 187774

African (AFR) AF: 0.00 AC: 0 AN: 7740

American (AMR) AF: 0.00 AC: 0 AN: 9262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9822

East Asian (EAS) AF: 0.00 AC: 0 AN: 18630

South Asian (SAS) AF: 0.00 AC: 0 AN: 31864

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17716

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1454

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 242452

Other (OTH) AF: 0.00 AC: 0 AN: 19678

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4058

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.58
PhyloP100		1.5

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;