rs10796459

Variant names:

• chr1-18150956-G-A
• rs10796459
• NM_032880.5:c.70+42758G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-18150956-G-A
• chr1-18150956-G-C

Variant summary

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

The NM_032880.5(IGSF21):​c.70+42758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,232 control chromosomes in the GnomAD database, including 60,504 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 0.89 (60504 hom., cov: 33)
• Consequence: IGSF21 NM_032880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF21	NM_032880.5	MANE Select	c.70+42758G>A		intron	N/A	NP_116269.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF21	ENST00000251296.4	TSL:1 MANE Select	c.70+42758G>A		intron	N/A	ENSP00000251296.1	Q96ID5
	IGSF21	ENST00000931381.1		c.70+42758G>A		intron	N/A	ENSP00000601440.1
	IGSF21	ENST00000873158.1		c.70+42758G>A		intron	N/A	ENSP00000543217.1

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135615 AN: 152114 Hom.: 60462 Cov.: 33

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.891 AC: 135711 AN: 152232 Hom.: 60504 Cov.: 33 AF XY: 0.892 AC XY: 66414 AN XY: 74430

African (AFR) AF: 0.889 AC: 36965 AN: 41558

American (AMR) AF: 0.910 AC: 13924 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4791 AN: 5150

South Asian (SAS) AF: 0.890 AC: 4290 AN: 4822

European-Finnish (FIN) AF: 0.908 AC: 9635 AN: 10608

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60336 AN: 68010

Other (OTH) AF: 0.883 AC: 1865 AN: 2112

Alfa AF: 0.888 Hom.: 8457

Bravo AF: 0.892

Asia WGS AF: 0.930 AC: 3234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.35
PhyloP100		-0.75
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: rs10796459; hg19: chr1-18477450;