rs210432

Variant names:

• chrX-105703303-A-C
• rs210432
• NM_017416.2:c.773-14064A>C

Your query was ambiguous. Multiple possible variants found:

• chrX-105703303-A-C
• chrX-105703303-A-T

Variant summary

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

The NM_017416.2(IL1RAPL2):​c.773-14064A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 109,537 control chromosomes in the GnomAD database, including 9,826 homozygotes. There are 13,791 hemizygotes in GnomAD. 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 0.45 (9826 hom., 13791 hem., cov: 22)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 2 publications found

Genes affected

IL1RAPL2 (HGNC:5997): (interleukin 1 receptor accessory protein like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [provided by RefSeq, Jul 2008]

LOC105373303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.773-14064A>C		intron_variant	Intron 6 of 10	ENST00000372582.6	NP_059112.1
LOC105373303	XR_007068300.1	n.4943T>G		non_coding_transcript_exon_variant	Exon 5 of 5
IL1RAPL2	XM_011530905.3	c.401-14064A>C		intron_variant	Intron 4 of 8		XP_011529207.1
LOC105373303	XR_938493.3	n.662+13971T>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.773-14064A>C		intron_variant	Intron 6 of 10	1	NM_017416.2	ENSP00000361663.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 49556 AN: 109486 Hom.: 9824 Cov.: 22

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.453 AC: 49609 AN: 109537 Hom.: 9826 Cov.: 22 AF XY: 0.431 AC XY: 13791 AN XY: 31985

African (AFR) AF: 0.785 AC: 23648 AN: 30121

American (AMR) AF: 0.292 AC: 2989 AN: 10244

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1069 AN: 2619

East Asian (EAS) AF: 0.277 AC: 946 AN: 3421

South Asian (SAS) AF: 0.372 AC: 952 AN: 2558

European-Finnish (FIN) AF: 0.250 AC: 1436 AN: 5755

Middle Eastern (MID) AF: 0.393 AC: 83 AN: 211

European-Non Finnish (NFE) AF: 0.334 AC: 17523 AN: 52453

Other (OTH) AF: 0.411 AC: 608 AN: 1478

Alfa AF: 0.338 Hom.: 8987

Bravo AF: 0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.41
PhyloP100		-0.91
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: rs210432; hg19: chrX-104947296;