rs773108294

Variant names:

• chr11-18706090-G-A
• rs773108294
• NM_173588.4:c.3637C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-18706090-G-A
• chr11-18706090-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_173588.4(IGSF22):​c.3637C>T​(p.Pro1213Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,548,500 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: IGSF22 NM_173588.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF22	NM_173588.4	c.3637C>T	p.Pro1213Ser	missense_variant	Exon 22 of 23	ENST00000513874.6	NP_775859.4
IGSF22	XM_047426830.1	c.1711C>T	p.Pro571Ser	missense_variant	Exon 9 of 10		XP_047282786.1
IGSF22	NR_160413.1	n.3393C>T		non_coding_transcript_exon_variant	Exon 20 of 21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGSF22	ENST00000513874.6	c.3637C>T	p.Pro1213Ser	missense_variant	Exon 22 of 23	5	NM_173588.4	ENSP00000421191.1
IGSF22	ENST00000319338.6	n.*533C>T		non_coding_transcript_exon_variant	Exon 20 of 21	2		ENSP00000322422.6
IGSF22	ENST00000510673.1	n.40C>T		non_coding_transcript_exon_variant	Exon 1 of 2	3
IGSF22	ENST00000319338.6	n.*533C>T		3_prime_UTR_variant	Exon 20 of 21	2		ENSP00000322422.6

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152224 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1396276 Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1 AN XY: 688930

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152224 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74368

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.047	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	22
DANN	Uncertain	1.0
Eigen	Uncertain	0.35
Eigen_PC	Benign	0.078
FATHMM_MKL	Benign	0.69	D
LIST_S2	Benign	0.57	T
M_CAP	Benign	0.069	D
MetaRNN	Uncertain	0.59	D
MetaSVM	Uncertain	0.12	D
PrimateAI	Benign	0.34	T
PROVEAN	Pathogenic	-6.7	D
REVEL	Uncertain	0.38
Sift	Uncertain	0.012	D
Sift4G	Pathogenic	0.0	D
Vest4		0.42
MVP		0.52
MPC		0.70
ClinPred		0.88	D
GERP RS		3.9
gMVP		0.95

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: rs773108294; hg19: chr11-18727637;