dbSNP rs2289965: IGSF22:p.Ile1131Val (chr11-18707103-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173588.4(IGSF22):c.3391A>G(p.Ile1131Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,551,224 control chromosomes in the GnomAD database, including 105,711 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 7854 hom., cov: 32)

Exomes 𝑓: 0.37 ( 97857 hom. )

Consequence

IGSF22
NM_173588.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990

Variant links:

Genes affected

IGSF22 (HGNC:26750): (immunoglobulin superfamily member 22)

IGSF22 links:

IGSF22-AS1 (HGNC:55511): (IGSF22 antisense RNA 1)

IGSF22-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.16656E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF22	NM_173588.4 link	c.3391A>G	p.Ile1131Val	missense_variant	Exon 21 of 23	ENST00000513874.6	NP_775859.4	Q8N9C0-2
IGSF22	XM_047426830.1 link	c.1465A>G	p.Ile489Val	missense_variant	Exon 8 of 10		XP_047282786.1
IGSF22	NR_160413.1 link	n.3147A>G		non_coding_transcript_exon_variant	Exon 19 of 21
IGSF22-AS1	NR_186353.1 link	n.623T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGSF22	ENST00000513874.6 link	c.3391A>G	p.Ile1131Val	missense_variant	Exon 21 of 23	5	NM_173588.4	ENSP00000421191.1		Q8N9C0-2

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43134

AN:

151984

Hom.:

7851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0705

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.325

AC:

50029

AN:

153960

Hom.:

9089

AF XY:

0.321

AC XY:

26192

AN XY:

81674

show subpopulations

Gnomad AFR exome

AF:

0.0580

Gnomad AMR exome

AF:

0.390

Gnomad ASJ exome

AF:

0.295

Gnomad EAS exome

AF:

0.147

Gnomad SAS exome

AF:

0.208

Gnomad FIN exome

AF:

0.464

Gnomad NFE exome

AF:

0.379

Gnomad OTH exome

AF:

0.325

GnomAD4 exome

AF:

0.365

AC:

510842

AN:

1399122

Hom.:

97857

Cov.:

AF XY:

0.361

AC XY:

249363

AN XY:

690090

show subpopulations

Gnomad4 AFR exome

AF:

0.0559

Gnomad4 AMR exome

AF:

0.379

Gnomad4 ASJ exome

AF:

0.294

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.211

Gnomad4 FIN exome

AF:

0.465

Gnomad4 NFE exome

AF:

0.391

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.284

AC:

43140

AN:

152102

Hom.:

7854

Cov.:

AF XY:

0.290

AC XY:

21548

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0703

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.382

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.356

Hom.:

24133

Bravo

AF:

0.266

TwinsUK

AF:

0.387

AC:

1434

ALSPAC

AF:

0.382

AC:

1473

ESP6500AA

AF:

0.0751

AC:

104

ESP6500EA

AF:

0.398

AC:

1267

ExAC

AF:

0.238

AC:

5771

Asia WGS

AF:

0.194

AC:

674

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.73

CADD

Benign

8.6

DANN

Benign

0.71

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.16

MetaRNN

Benign

0.00012

MetaSVM

Benign

-0.94

PrimateAI

Benign

0.38

PROVEAN

Benign

0.74

REVEL

Benign

0.037

Sift

Benign

1.0

Sift4G

Benign

1.0

Vest4

0.010

MPC

0.18

ClinPred

0.0021

GERP RS

2.5

gMVP

0.16

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over