1-160887174-A-G

Variant names:

• chr1-160887174-A-G
• rs4656958
• ENST00000896872.1:c.-6-2291T>C

Variant summary

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

The ENST00000896872.1(ITLN1):​c.-6-2291T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,908 control chromosomes in the GnomAD database, including 33,261 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 0.66 (33261 hom., cov: 30)
• Consequence: ITLN1 ENST00000896872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 51 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000896872.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITLN1	ENST00000896872.1		c.-6-2291T>C		intron	N/A	ENSP00000566931.1
	ITLN1	ENST00000896873.1		c.-7+483T>C		intron	N/A	ENSP00000566932.1
	ITLN1	ENST00000896874.1		c.-45+483T>C		intron	N/A	ENSP00000566933.1

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100034 AN: 151790 Hom.: 33245 Cov.: 30

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.659 AC: 100101 AN: 151908 Hom.: 33261 Cov.: 30 AF XY: 0.661 AC XY: 49108 AN XY: 74248

African (AFR) AF: 0.563 AC: 23297 AN: 41378

American (AMR) AF: 0.707 AC: 10799 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3708 AN: 5154

South Asian (SAS) AF: 0.687 AC: 3307 AN: 4812

European-Finnish (FIN) AF: 0.692 AC: 7312 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46740 AN: 67946

Other (OTH) AF: 0.667 AC: 1411 AN: 2114

Alfa AF: 0.652 Hom.: 20674

Bravo AF: 0.657

Asia WGS AF: 0.662 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs4656958; hg19: chr1-160856964;