rs1555001

Variant names:

• chr16-3067353-T-A
• rs1555001
• NM_001376923.1:c.16-24T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3067353-T-A
• chr16-3067353-T-C
• chr16-3067353-T-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001376923.1(IL32):​c.16-24T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,397,976 control chromosomes in the GnomAD database, including 81,628 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. There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.31 (7669 hom., cov: 29)
  • Exomes 𝑓: 0.33 (73959 hom.)
• Consequence: IL32 NM_001376923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 17 publications found

Genes affected

IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1	c.16-24T>A		intron_variant	Intron 2 of 6	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.16-24T>A		intron_variant	Intron 2 of 6	1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46066 AN: 150512 Hom.: 7670 Cov.: 29

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.287

GnomAD2 exomes AF: 0.361 AC: 66992 AN: 185498 AF XY: 0.365

Gnomad AFR exome AF: 0.204

Gnomad AMR exome AF: 0.473

Gnomad ASJ exome AF: 0.275

Gnomad EAS exome AF: 0.389

Gnomad FIN exome AF: 0.368

Gnomad NFE exome AF: 0.316

Gnomad OTH exome AF: 0.338

GnomAD4 exome AF: 0.334 AC: 416028 AN: 1247342 Hom.: 73959 Cov.: 18 AF XY: 0.340 AC XY: 210359 AN XY: 618406

African (AFR) AF: 0.197 AC: 5439 AN: 27672

American (AMR) AF: 0.459 AC: 14411 AN: 31406

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 5140 AN: 19692

East Asian (EAS) AF: 0.456 AC: 17503 AN: 38342

South Asian (SAS) AF: 0.592 AC: 41126 AN: 69430

European-Finnish (FIN) AF: 0.379 AC: 18965 AN: 50024

Middle Eastern (MID) AF: 0.283 AC: 1431 AN: 5052

European-Non Finnish (NFE) AF: 0.309 AC: 294924 AN: 953452

Other (OTH) AF: 0.327 AC: 17089 AN: 52272

GnomAD4 genome AF: 0.306 AC: 46081 AN: 150634 Hom.: 7669 Cov.: 29 AF XY: 0.314 AC XY: 23076 AN XY: 73378

African (AFR) AF: 0.202 AC: 8299 AN: 41034

American (AMR) AF: 0.377 AC: 5718 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2009 AN: 5036

South Asian (SAS) AF: 0.603 AC: 2885 AN: 4784

European-Finnish (FIN) AF: 0.379 AC: 3844 AN: 10142

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21446 AN: 67726

Other (OTH) AF: 0.287 AC: 598 AN: 2084

Alfa AF: 0.229 Hom.: 689

Bravo AF: 0.294

Asia WGS AF: 0.476 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.71
PhyloP100		0.12
BranchPoint Hunter		5.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.24		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.24		Position offset: 2

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

Other links and lift over

dbSNP: rs1555001; hg19: chr16-3117354; COSMIC: COSV50403951; COSMIC: COSV50403951;