chr3-52783577-T-C

Variant names:

• chr3-52783577-T-C
• rs2710322
• NM_002215.4:c.1225+238T>C

Variant summary

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

The NM_002215.4(ITIH1):​c.1225+238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,208 control chromosomes in the GnomAD database, including 56,917 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 0.86 (56917 hom., cov: 32)
• Consequence: ITIH1 NM_002215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 12 publications found

Genes affected

ITIH1 (HGNC:6166): (inter-alpha-trypsin inhibitor heavy chain 1) This gene encodes a member of the inter-alpha-trypsin inhibitor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the heavy chain of the inter-alpha-trypsin inhibitor complex, which is secreted by hepatocytes into the blood. The heavy chain also interacts with hyaluronan, and this interaction may play a role in ovulation and fertilization, and has been implicated in multiple inflammatory diseases. This gene is present in a gene cluster on chromosome 3. [provided by RefSeq, Nov 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002215.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITIH1	NM_002215.4	MANE Select	c.1225+238T>C		intron	N/A	NP_002206.2
	ITIH1	NM_001166434.3		c.799+238T>C		intron	N/A	NP_001159906.1
	ITIH1	NM_001166435.2		c.361+238T>C		intron	N/A	NP_001159907.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITIH1	ENST00000273283.7	TSL:1 MANE Select	c.1225+238T>C		intron	N/A	ENSP00000273283.2
	ITIH1	ENST00000537050.5	TSL:2	c.361+238T>C		intron	N/A	ENSP00000443847.1
	ITIH1	ENST00000628722.2	TSL:2	n.1080+238T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131323 AN: 152090 Hom.: 56872 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.863 AC: 131423 AN: 152208 Hom.: 56917 Cov.: 32 AF XY: 0.860 AC XY: 64005 AN XY: 74422

African (AFR) AF: 0.877 AC: 36432 AN: 41522

American (AMR) AF: 0.858 AC: 13125 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3079 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3766 AN: 5170

South Asian (SAS) AF: 0.659 AC: 3176 AN: 4818

European-Finnish (FIN) AF: 0.894 AC: 9486 AN: 10610

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59504 AN: 68002

Other (OTH) AF: 0.854 AC: 1806 AN: 2114

Alfa AF: 0.863 Hom.: 48707

Bravo AF: 0.862

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.60
PhyloP100		-2.3
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: rs2710322; hg19: chr3-52817593;