rs223185

Variant names:

• chr1-18258526-T-A
• rs223185
• NM_032880.5:c.183+30516T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-18258526-T-A
• chr1-18258526-T-C
• chr1-18258526-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032880.5(IGSF21):​c.183+30516T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,044 control chromosomes in the GnomAD database, including 9,737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (9737 hom., cov: 32)
• Consequence: IGSF21 NM_032880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

Genes affected

IGSF21 (HGNC:28246): (immunoglobin superfamily member 21) This gene encodes a protein which has two immunoglobulin (Ig) domains and is a member of the immunoglobulin superfamily. Proteins in this superfamily are usually found on or in cell membranes and act as receptors in immune response pathways. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032880.5. 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
	IGSF21	NM_032880.5	MANE Select	c.183+30516T>A		intron	N/A	NP_116269.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF21	ENST00000251296.4	TSL:1 MANE Select	c.183+30516T>A		intron	N/A	ENSP00000251296.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53527 AN: 151926 Hom.: 9719 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.356

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.353 AC: 53601 AN: 152044 Hom.: 9737 Cov.: 32 AF XY: 0.345 AC XY: 25654 AN XY: 74312

African (AFR) AF: 0.399 AC: 16533 AN: 41462

American (AMR) AF: 0.317 AC: 4845 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3472

East Asian (EAS) AF: 0.106 AC: 550 AN: 5178

South Asian (SAS) AF: 0.203 AC: 977 AN: 4814

European-Finnish (FIN) AF: 0.333 AC: 3513 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24960 AN: 67968

Other (OTH) AF: 0.356 AC: 751 AN: 2112

Alfa AF: 0.222 Hom.: 491

Bravo AF: 0.354

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.85
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs223185; hg19: chr1-18585020;