Genetic Variant VSIG10:p.Glu473_Glu474del (chr12-118068522-TTCCTCC-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_019086.6(VSIG10):c.1416_1421delGGAGGA(p.Glu473_Glu474del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,602,096 control chromosomes in the GnomAD database, including 35,263 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 5081 hom., cov: 19)

Exomes 𝑓: 0.20 ( 30182 hom. )

Consequence

VSIG10
NM_019086.6 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.61

Publications

3 publications found

Variant links:

Genes affected

VSIG10 (HGNC:26078): (V-set and immunoglobulin domain containing 10) Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be active in cell-cell junction. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

VSIG10 links:

LOC124903030 (HGNC:):

LOC124903030 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 12-118068522-TTCCTCC-T is Benign according to our data. Variant chr12-118068522-TTCCTCC-T is described in ClinVar as [Benign]. Clinvar id is 403604.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSIG10	NM_019086.6 link	c.1416_1421delGGAGGA	p.Glu473_Glu474del	disruptive_inframe_deletion	Exon 8 of 9	ENST00000359236.10	NP_061959.2	Q8N0Z9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSIG10	ENST00000359236.10 link	c.1416_1421delGGAGGA	p.Glu473_Glu474del	disruptive_inframe_deletion	Exon 8 of 9	1	NM_019086.6	ENSP00000352172.5		Q8N0Z9-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37042

AN:

150576

Hom.:

5071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.532

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.266

GnomAD2 exomes

AF:

0.229

AC:

49617

AN:

216714

AF XY:

0.225

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.179

Gnomad EAS exome

AF:

0.518

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.190

Gnomad OTH exome

AF:

0.231

GnomAD4 exome

AF:

0.202

AC:

293192

AN:

1451408

Hom.:

30182

AF XY:

0.202

AC XY:

145441

AN XY:

721440

show subpopulations

African (AFR)

AF:

0.330

AC:

10961

AN:

33176

American (AMR)

AF:

0.201

AC:

8640

AN:

42964

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

4519

AN:

25942

East Asian (EAS)

AF:

0.501

AC:

19512

AN:

38976

South Asian (SAS)

AF:

0.206

AC:

17575

AN:

85286

European-Finnish (FIN)

AF:

0.179

AC:

9478

AN:

53052

Middle Eastern (MID)

AF:

0.200

AC:

1151

AN:

5750

European-Non Finnish (NFE)

AF:

0.189

AC:

208577

AN:

1106258

Other (OTH)

AF:

0.213

AC:

12779

AN:

60004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

13264

26529

39793

53058

66322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7664

15328

22992

30656

38320

<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:

0.246

AC:

37077

AN:

150688

Hom.:

5081

Cov.:

AF XY:

0.245

AC XY:

17979

AN XY:

73528

show subpopulations

African (AFR)

AF:

0.332

AC:

13592

AN:

40990

American (AMR)

AF:

0.232

AC:

3497

AN:

15086

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

638

AN:

3462

East Asian (EAS)

AF:

0.532

AC:

2695

AN:

5062

South Asian (SAS)

AF:

0.216

AC:

1029

AN:

4758

European-Finnish (FIN)

AF:

0.181

AC:

1877

AN:

10384

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.189

AC:

12798

AN:

67666

Other (OTH)

AF:

0.263

AC:

548

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1289

2577

3866

5154

6443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<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:

0.130

Hom.:

263

Bravo

AF:

0.260

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Mutation Taster

=191/9

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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12-118068522-TTCCTCCTCCTCC-TTCCTCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over