rs17318858

chr11-10558140-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006691.4(LYVE1):c.*971A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,118 control chromosomes in the GnomAD database, including 2,390 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 0.15 (2389 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LYVE1 NM_006691.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

Genes affected

LYVE1 (HGNC:14687): (lymphatic vessel endothelial hyaluronan receptor 1) This gene encodes a type I integral membrane glycoprotein. The encoded protein acts as a receptor and binds to both soluble and immobilized hyaluronan. This protein may function in lymphatic hyaluronan transport and have a role in tumor metastasis. [provided by RefSeq, Jul 2008]

IRAG1-AS1 (HGNC:43434): (IRAG1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYVE1	NM_006691.4	c.*971A>G		3_prime_UTR_variant	6/6	ENST00000256178.8
IRAG1-AS1	NR_046374.1	n.307+16598T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYVE1	ENST00000256178.8	c.*971A>G		3_prime_UTR_variant	6/6	1	NM_006691.4	P1
IRAG1-AS1	ENST00000663840.1	n.285+16598T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23242 AN: 151998 Hom.: 2388 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0701

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.153 AC: 23241 AN: 152116 Hom.: 2389 Cov.: 32 AF XY: 0.151 AC XY: 11264 AN XY: 74372

Gnomad4 AFR AF: 0.0405

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.135

Alfa AF: 0.209 Hom.: 3194

Bravo AF: 0.144

Asia WGS AF: 0.0400 AC: 140 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.8
Dann	Benign	0.83

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

Other links and lift over

dbSNP: rs17318858; hg19: chr11-10579687;