11-18707043-TGAA-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3 BP6_Moderate BS2

The NM_173588.4(IGSF22):c.3448_3450del(p.Phe1150del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00254 in 1,551,708 control chromosomes in the GnomAD database, including 12 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0026 (11 hom.)
• Consequence: IGSF22 NM_173588.4 inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.11

Genes affected

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

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

TMEM86A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_173588.4
• BP6: Variant 11-18707043-TGAA-T is Benign according to our data. Variant chr11-18707043-TGAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641666.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGSF22	NM_173588.4	c.3448_3450del	p.Phe1150del	inframe_deletion	21/23	ENST00000513874.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGSF22	ENST00000513874.6	c.3448_3450del	p.Phe1150del	inframe_deletion	21/23	5	NM_173588.4	P1
IGSF22	ENST00000504981.5	n.3788_3790del		non_coding_transcript_exon_variant	20/20	1
IGSF22-AS1	ENST00000527285.1	n.510_512del		non_coding_transcript_exon_variant	1/3	3
IGSF22	ENST00000319338.6	c.*344_*346del		3_prime_UTR_variant, NMD_transcript_variant	19/21	2

Frequencies

GnomAD3 genomes AF: 0.00185 AC: 281 AN: 152218 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000434

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00164

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00284

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00216 AC: 333 AN: 154028 Hom.: 4 AF XY: 0.00196 AC XY: 160 AN XY: 81702

Gnomad AFR exome AF: 0.000378

Gnomad AMR exome AF: 0.00158

Gnomad ASJ exome AF: 0.00778

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00132

Gnomad FIN exome AF: 0.000262

Gnomad NFE exome AF: 0.00293

Gnomad OTH exome AF: 0.00369

GnomAD4 exome AF: 0.00262 AC: 3661 AN: 1399372 Hom.: 11 AF XY: 0.00258 AC XY: 1784 AN XY: 690194

Gnomad4 AFR exome AF: 0.000443

Gnomad4 AMR exome AF: 0.00168

Gnomad4 ASJ exome AF: 0.00691

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00172

Gnomad4 FIN exome AF: 0.000406

Gnomad4 NFE exome AF: 0.00283

Gnomad4 OTH exome AF: 0.00303

GnomAD4 genome AF: 0.00184 AC: 281 AN: 152336 Hom.: 1 Cov.: 31 AF XY: 0.00179 AC XY: 133 AN XY: 74492

Gnomad4 AFR AF: 0.000433

Gnomad4 AMR AF: 0.00163

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00284

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00262 Hom.: 0

Bravo AF: 0.00190

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

IGSF22: BS2 -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs543347161; hg19: chr11-18728590;