chr1-160882256-T-C

Variant names:

• chr1-160882256-T-C
• rs2274910
• NM_017625.3:c.158-52A>G

Variant summary

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

The NM_017625.3(ITLN1):​c.158-52A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,982 control chromosomes in the GnomAD database, including 27,859 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 0.59 (27859 hom., cov: 31)
  • Exomes 𝑓: 0.67 (310190 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITLN1 NM_017625.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 84 publications found

Genes affected

ITLN1 (HGNC:18259): (intelectin 1) Enables calcium ion binding activity; identical protein binding activity; and oligosaccharide binding activity. Involved in positive regulation of glucose import; positive regulation of protein phosphorylation; and protein homotrimerization. Located in extracellular exosome. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017625.3. 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
	ITLN1	NM_017625.3	MANE Select	c.158-52A>G		intron	N/A	NP_060095.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITLN1	ENST00000326245.4	TSL:1 MANE Select	c.158-52A>G		intron	N/A	ENSP00000323587.3	Q8WWA0
	ITLN1	ENST00000896872.1		c.158-52A>G		intron	N/A	ENSP00000566931.1
	ITLN1	ENST00000896873.1		c.158-52A>G		intron	N/A	ENSP00000566932.1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89003 AN: 151864 Hom.: 27855 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.623

GnomAD2 exomes AF: 0.650 AC: 116821 AN: 179682 AF XY: 0.655

Gnomad AFR exome AF: 0.326

Gnomad AMR exome AF: 0.719

Gnomad ASJ exome AF: 0.743

Gnomad EAS exome AF: 0.680

Gnomad FIN exome AF: 0.691

Gnomad NFE exome AF: 0.673

Gnomad OTH exome AF: 0.667

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.670 AC: 919189 AN: 1372464 Hom.: 310190 Cov.: 35 AF XY: 0.670 AC XY: 450929 AN XY: 673002

African (AFR) AF: 0.326 AC: 9951 AN: 30480

American (AMR) AF: 0.713 AC: 22483 AN: 31520

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 14752 AN: 20294

East Asian (EAS) AF: 0.660 AC: 25645 AN: 38874

South Asian (SAS) AF: 0.628 AC: 44906 AN: 71518

European-Finnish (FIN) AF: 0.686 AC: 34190 AN: 49872

Middle Eastern (MID) AF: 0.708 AC: 3770 AN: 5324

European-Non Finnish (NFE) AF: 0.680 AC: 726397 AN: 1068136

Other (OTH) AF: 0.657 AC: 37095 AN: 56446

GnomAD4 genome AF: 0.586 AC: 89040 AN: 151982 Hom.: 27859 Cov.: 31 AF XY: 0.588 AC XY: 43691 AN XY: 74278

African (AFR) AF: 0.336 AC: 13926 AN: 41410

American (AMR) AF: 0.675 AC: 10315 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2529 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3491 AN: 5170

South Asian (SAS) AF: 0.626 AC: 3018 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7312 AN: 10572

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 46227 AN: 67954

Other (OTH) AF: 0.621 AC: 1312 AN: 2112

Alfa AF: 0.651 Hom.: 112413

Bravo AF: 0.577

Asia WGS AF: 0.585 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.89
PhyloP100		-0.32
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: rs2274910; hg19: chr1-160852046; COSMIC: COSV58275465; COSMIC: COSV58275465;