rs17403795

Variant names:

• chr11-10559670-G-A
• rs17403795
• NM_006691.4:c.782+146C>T

Variant summary

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

The NM_006691.4(LYVE1):​c.782+146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 640,598 control chromosomes in the GnomAD database, including 3,884 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 0.092 (799 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3085 hom.)
• Consequence: LYVE1 NM_006691.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYVE1	NM_006691.4	c.782+146C>T		intron_variant	Intron 5 of 5	ENST00000256178.8	NP_006682.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYVE1	ENST00000256178.8	c.782+146C>T		intron_variant	Intron 5 of 5	1	NM_006691.4	ENSP00000256178.3

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13954 AN: 152066 Hom.: 799 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.00789

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0923

GnomAD4 exome AF: 0.104 AC: 50580 AN: 488414 Hom.: 3085 AF XY: 0.103 AC XY: 26381 AN XY: 256204

Gnomad4 AFR exome AF: 0.0341

Gnomad4 AMR exome AF: 0.138

Gnomad4 ASJ exome AF: 0.0516

Gnomad4 EAS exome AF: 0.00657

Gnomad4 SAS exome AF: 0.0918

Gnomad4 FIN exome AF: 0.138

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.0966

GnomAD4 genome AF: 0.0917 AC: 13957 AN: 152184 Hom.: 799 Cov.: 32 AF XY: 0.0922 AC XY: 6861 AN XY: 74406

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.00791

Gnomad4 SAS AF: 0.0866

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.107 Hom.: 1312

Bravo AF: 0.0870

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs17403795; hg19: chr11-10581217;