Variant chr11-18707941-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_173588.4(IGSF22):c.3143G>A(p.Arg1048Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00529 in 1,614,180 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0054 ( 40 hom. )

Consequence

IGSF22
NM_173588.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.541

Variant links:

Genes affected

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

IGSF22 links:

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

IGSF22-AS1 links:

TMEM86A (HGNC:):

TMEM86A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00561291).

BP6

Variant 11-18707941-C-T is Benign according to our data. Variant chr11-18707941-C-T is described in ClinVar as [Benign]. Clinvar id is 2641667.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGSF22	NM_173588.4 linkuse as main transcript	c.3143G>A	p.Arg1048Gln	missense_variant	20/23	ENST00000513874.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGSF22	ENST00000513874.6 linkuse as main transcript	c.3143G>A	p.Arg1048Gln	missense_variant	20/23	5	NM_173588.4	P1	Q8N9C0-2
IGSF22	ENST00000504981.5 linkuse as main transcript	n.3483G>A		non_coding_transcript_exon_variant	19/20	1
IGSF22-AS1	ENST00000527285.1 linkuse as main transcript	n.729+548C>T		intron_variant, non_coding_transcript_variant		3
IGSF22	ENST00000319338.6 linkuse as main transcript	c.*39G>A		3_prime_UTR_variant, NMD_transcript_variant	18/21	2			Q8N9C0-1

Frequencies

GnomAD3 genomes

AF:

0.00392

AC:

597

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00766

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00653

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00403

AC:

1007

AN:

249578

Hom.:

AF XY:

0.00458

AC XY:

620

AN XY:

135404

show subpopulations

Gnomad AFR exome

AF:

0.000969

Gnomad AMR exome

AF:

0.00235

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00650

Gnomad FIN exome

AF:

0.00199

Gnomad NFE exome

AF:

0.00573

Gnomad OTH exome

AF:

0.00280

GnomAD4 exome

AF:

0.00543

AC:

7944

AN:

1461862

Hom.:

Cov.:

AF XY:

0.00551

AC XY:

4004

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.000836

Gnomad4 AMR exome

AF:

0.00212

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00711

Gnomad4 FIN exome

AF:

0.00219

Gnomad4 NFE exome

AF:

0.00612

Gnomad4 OTH exome

AF:

0.00426

GnomAD4 genome

AF:

0.00393

AC:

598

AN:

152318

Hom.:

Cov.:

AF XY:

0.00367

AC XY:

273

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00787

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.00653

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00505

Hom.:

Bravo

AF:

0.00379

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00649

AC:

ESP6500AA

AF:

0.00149

AC:

ESP6500EA

AF:

0.00657

AC:

ExAC

AF:

0.00443

AC:

536

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

IGSF22: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.72

FATHMM_MKL

Benign

0.085

LIST_S2

Benign

0.63

M_CAP

Benign

0.013

MetaRNN

Benign

0.0056

MetaSVM

Benign

-0.91

MutationTaster

Benign

1.0

PrimateAI

Benign

0.21

PROVEAN

Uncertain

-2.6

REVEL

Benign

0.17

Sift

Uncertain

0.011

Sift4G

Uncertain

0.040

Vest4

0.39

MVP

0.24

MPC

0.31

ClinPred

0.023

GERP RS

1.8

gMVP

0.38

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over