Genetic Variant NM_006691.4:c.782+146C>T (chr11-10559670-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Publications

7 publications found

Variant links:

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]

LYVE1 links:

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

IRAG1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LYVE1	NM_006691.4	MANE Select	c.782+146C>T	intron	N/A	NP_006682.2
IRAG1-AS1	NR_034093.2		n.307+18128G>A	intron	N/A
IRAG1-AS1	NR_034094.2		n.307+18128G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LYVE1	ENST00000256178.8	TSL:1 MANE Select	c.782+146C>T	intron	N/A	ENSP00000256178.3	Q9Y5Y7
LYVE1	ENST00000860862.1		c.476+146C>T	intron	N/A	ENSP00000530921.1
LYVE1	ENST00000529598.1	TSL:2	c.470+146C>T	intron	N/A	ENSP00000436016.1	F2Z296

Frequencies

GnomAD3 genomes

AF:

0.0918

AC:

13954

AN:

152066

Hom.:

799

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.0341

AC:

446

AN:

13094

American (AMR)

AF:

0.138

AC:

2617

AN:

18934

Ashkenazi Jewish (ASJ)

AF:

0.0516

AC:

722

AN:

13998

East Asian (EAS)

AF:

0.00657

AC:

202

AN:

30744

South Asian (SAS)

AF:

0.0918

AC:

3965

AN:

43210

European-Finnish (FIN)

AF:

0.138

AC:

4969

AN:

35900

Middle Eastern (MID)

AF:

0.0467

AC:

150

AN:

3214

European-Non Finnish (NFE)

AF:

0.115

AC:

34881

AN:

302126

Other (OTH)

AF:

0.0966

AC:

2628

AN:

27194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2135

4270

6405

8540

10675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

362

724

1086

1448

1810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0917

AC:

13957

AN:

152184

Hom.:

799

Cov.:

AF XY:

0.0922

AC XY:

6861

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0335

AC:

1392

AN:

41522

American (AMR)

AF:

0.144

AC:

2207

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0499

AC:

173

AN:

3468

East Asian (EAS)

AF:

0.00791

AC:

AN:

5182

South Asian (SAS)

AF:

0.0866

AC:

418

AN:

4828

European-Finnish (FIN)

AF:

0.130

AC:

1373

AN:

10570

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8049

AN:

68006

Other (OTH)

AF:

0.0937

AC:

198

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

634

1268

1901

2535

3169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.105

Hom.:

1617

Bravo

AF:

0.0870

Asia WGS

AF:

0.0670

AC:

232

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.9

(source)

DANN

Benign

0.49

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over