rs17318858

Variant names:

• chr11-10558140-T-C
• rs17318858
• NM_006691.4:c.*971A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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.*971A>G		3_prime_UTR	Exon 6 of 6	NP_006682.2
	IRAG1-AS1	NR_034093.2		n.307+16598T>C		intron	N/A
	IRAG1-AS1	NR_034094.2		n.307+16598T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYVE1	ENST00000256178.8	TSL:1 MANE Select	c.*971A>G		3_prime_UTR	Exon 6 of 6	ENSP00000256178.3	Q9Y5Y7
	LYVE1	ENST00000860862.1		c.*971A>G		3_prime_UTR	Exon 5 of 5	ENSP00000530921.1
	IRAG1-AS1	ENST00000529829.8	TSL:2	n.299+16598T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

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: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0405 AC: 1682 AN: 41532

American (AMR) AF: 0.149 AC: 2281 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0718 AC: 347 AN: 4830

European-Finnish (FIN) AF: 0.225 AC: 2372 AN: 10560

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15153 AN: 67964

Other (OTH) AF: 0.135 AC: 284 AN: 2104

Alfa AF: 0.189 Hom.: 3972

Bravo AF: 0.144

Asia WGS AF: 0.0400 AC: 140 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.8
DANN	Benign	0.83
PhyloP100		0.044
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: rs17318858; hg19: chr11-10579687;