rs17403620

chr11-10557561-G-A

Variant summary

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

The NM_006691.4(LYVE1):c.*1550C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 152,130 control chromosomes in the GnomAD database, including 483 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 0.068 (483 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: LYVE1 NM_006691.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYVE1	NM_006691.4	c.*1550C>T		3_prime_UTR_variant	6/6	ENST00000256178.8
IRAG1-AS1	NR_046374.1	n.307+16019G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYVE1	ENST00000256178.8	c.*1550C>T		3_prime_UTR_variant	6/6	1	NM_006691.4	P1
IRAG1-AS1	ENST00000663840.1	n.285+16019G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10309 AN: 151986 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.0637

GnomAD4 exome AF: 0.115 AC: 3 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0678 AC: 10311 AN: 152104 Hom.: 483 Cov.: 32 AF XY: 0.0682 AC XY: 5069 AN XY: 74356

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0670

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0856 Hom.: 760

Bravo AF: 0.0586

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4
Dann	Benign	0.90

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: rs17403620; hg19: chr11-10579108;