rs17403620

Variant names:

• chr11-10557561-G-A
• rs17403620
• NM_006691.4:c.*1550C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006691.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYVE1	NM_006691.4	MANE Select	c.*1550C>T		3_prime_UTR	Exon 6 of 6	NP_006682.2
	IRAG1-AS1	NR_034093.2		n.307+16019G>A		intron	N/A
	IRAG1-AS1	NR_034094.2		n.307+16019G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYVE1	ENST00000256178.8	TSL:1 MANE Select	c.*1550C>T		3_prime_UTR	Exon 6 of 6	ENSP00000256178.3	Q9Y5Y7
	LYVE1	ENST00000860862.1		c.*1550C>T		3_prime_UTR	Exon 5 of 5	ENSP00000530921.1
	IRAG1-AS1	ENST00000529829.8	TSL:2	n.299+16019G>A		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.136 AC: 3 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0176 AC: 731 AN: 41492

American (AMR) AF: 0.0670 AC: 1023 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1325 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0971 AC: 6601 AN: 67984

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0827 Hom.: 913

Bravo AF: 0.0586

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.90
PhyloP100		-0.63
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: rs17403620; hg19: chr11-10579108;