1-160882256-T-C

Position:

• chr1-160882256-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITLN1	NM_017625.3	c.158-52A>G		intron_variant		ENST00000326245.4	NP_060095.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITLN1	ENST00000326245.4	c.158-52A>G		intron_variant		1	NM_017625.3	ENSP00000323587.3
ITLN1	ENST00000464077.1	n.40A>G		non_coding_transcript_exon_variant	1/2	2

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

GnomAD3 exomes AF: 0.650 AC: 116821 AN: 179682 Hom.: 38848 AF XY: 0.655 AC XY: 62020 AN XY: 94738

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 SAS exome AF: 0.632

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

Gnomad4 AFR exome AF: 0.326

Gnomad4 AMR exome AF: 0.713

Gnomad4 ASJ exome AF: 0.727

Gnomad4 EAS exome AF: 0.660

Gnomad4 SAS exome AF: 0.628

Gnomad4 FIN exome AF: 0.686

Gnomad4 NFE exome AF: 0.680

Gnomad4 OTH exome AF: 0.657

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.621

Alfa AF: 0.667 Hom.: 51818

Bravo AF: 0.577

Asia WGS AF: 0.585 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.89

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

Publications

LitVar

Other links and lift over

dbSNP: rs2274910; hg19: chr1-160852046; COSMIC: COSV58275465; COSMIC: COSV58275465;