rs10832975

Variant names:

• chr11-18721633-C-A
• rs10832975
• NM_173588.4:c.280G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-18721633-C-A
• chr11-18721633-C-G
• chr11-18721633-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_173588.4(IGSF22):​c.280G>T​(p.Ala94Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 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: not found (cov: 33)
• Consequence: IGSF22 NM_173588.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.57
• Publications: 25 publications found

Genes affected

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

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24588665).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173588.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF22	NM_173588.4	MANE Select	c.280G>T	p.Ala94Ser	missense	Exon 4 of 23	NP_775859.4
	IGSF22	NR_160413.1		n.428G>T		non_coding_transcript_exon	Exon 4 of 21
	IGSF22-AS1	NR_186353.1		n.785+14240C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF22	ENST00000513874.6	TSL:5 MANE Select	c.280G>T	p.Ala94Ser	missense	Exon 4 of 23	ENSP00000421191.1
	IGSF22	ENST00000504981.5	TSL:1	n.421G>T		non_coding_transcript_exon	Exon 4 of 20
	IGSF22	ENST00000319338.6	TSL:2	n.280G>T		non_coding_transcript_exon	Exon 4 of 21	ENSP00000322422.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 56

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 3161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.083	T
BayesDel_noAF	Benign	-0.36
CADD	Benign	22
DANN	Uncertain	1.0
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.090
FATHMM_MKL	Benign	0.66	D
LIST_S2	Benign	0.23	T
M_CAP	Uncertain	0.091	D
MetaRNN	Benign	0.25	T
MetaSVM	Benign	-0.77	T
PhyloP100		5.6
PrimateAI	Benign	0.35	T
PROVEAN	Benign	0.17	N
REVEL	Benign	0.15
Sift	Benign	0.036	D
Sift4G	Uncertain	0.045	D
Vest4		0.18
MutPred		0.65		Gain of disorder (P = 0.0358)
MVP		0.72
MPC		0.23
ClinPred		0.99	D
GERP RS		4.4
gMVP		0.58
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10832975; hg19: chr11-18743180;