Genetic Variant VSIG10:p.Glu474del (chr12-118068522-TTCC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_019086.6(VSIG10):c.1419_1421delGGA(p.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 0.0262 in 1,570,240 control chromosomes in the GnomAD database, including 468 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.019 ( 23 hom., cov: 19)

Exomes 𝑓: 0.027 ( 445 hom. )

Consequence

VSIG10
NM_019086.6 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0193 (2904/150750) while in subpopulation NFE AF = 0.029 (1963/67680). AF 95% confidence interval is 0.0279. There are 23 homozygotes in GnomAd4. There are 1400 alleles in the male GnomAd4 subpopulation. Median coverage is 19. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 23 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSIG10	NM_019086.6 link	c.1419_1421delGGA	p.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.1419_1421delGGA	p.Glu474del	disruptive_inframe_deletion	Exon 8 of 9	1	NM_019086.6	ENSP00000352172.5		Q8N0Z9-1

Frequencies

GnomAD3 genomes

AF:

0.0193

AC:

2903

AN:

150638

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00672

Gnomad AMI

AF:

0.00442

Gnomad AMR

AF:

0.0182

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.00295

Gnomad SAS

AF:

0.0134

Gnomad FIN

AF:

0.0192

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0290

Gnomad OTH

AF:

0.0208

GnomAD2 exomes

AF:

0.0230

AC:

4980

AN:

216714

AF XY:

0.0235

show subpopulations

Gnomad AFR exome

AF:

0.00657

Gnomad AMR exome

AF:

0.0177

Gnomad ASJ exome

AF:

0.0228

Gnomad EAS exome

AF:

0.00604

Gnomad FIN exome

AF:

0.0218

Gnomad NFE exome

AF:

0.0307

Gnomad OTH exome

AF:

0.0245

GnomAD4 exome

AF:

0.0270

AC:

38287

AN:

1419490

Hom.:

445

AF XY:

0.0267

AC XY:

18817

AN XY:

705072

show subpopulations

African (AFR)

AF:

0.00819

AC:

267

AN:

32608

American (AMR)

AF:

0.0169

AC:

705

AN:

41686

Ashkenazi Jewish (ASJ)

AF:

0.0188

AC:

472

AN:

25084

East Asian (EAS)

AF:

0.00804

AC:

309

AN:

38424

South Asian (SAS)

AF:

0.0168

AC:

1381

AN:

82006

European-Finnish (FIN)

AF:

0.0219

AC:

1125

AN:

51466

Middle Eastern (MID)

AF:

0.0436

AC:

246

AN:

5638

European-Non Finnish (NFE)

AF:

0.0299

AC:

32388

AN:

1084120

Other (OTH)

AF:

0.0238

AC:

1394

AN:

58458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

2061

4123

6184

8246

10307

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1196

2392

3588

4784

5980

<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:

0.0193

AC:

2904

AN:

150750

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1400

AN XY:

73554

show subpopulations

African (AFR)

AF:

0.00675

AC:

277

AN:

41028

American (AMR)

AF:

0.0182

AC:

274

AN:

15094

Ashkenazi Jewish (ASJ)

AF:

0.0170

AC:

AN:

3464

East Asian (EAS)

AF:

0.00296

AC:

AN:

5068

South Asian (SAS)

AF:

0.0134

AC:

AN:

4760

European-Finnish (FIN)

AF:

0.0192

AC:

199

AN:

10372

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0290

AC:

1963

AN:

67680

Other (OTH)

AF:

0.0206

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

142

284

425

567

709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0244

Hom.:

263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Mutation Taster

=83/17

polymorphism

(source)

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

Publications

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12-118068522-TTCCTCCTCCTCC-TTCCTCCTCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over