10-7563220-C-G

Variant names:

• chr10-7563220-C-G
• NM_030569.7:c.2692G>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_030569.7(ITIH5):​c.2692G>C​(p.Gly898Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ITIH5 NM_030569.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.46

Genes affected

ITIH5 (HGNC:21449): (inter-alpha-trypsin inhibitor heavy chain 5) This gene encodes a heavy chain component of one of the inter-alpha-trypsin inhibitor (ITI) family members. ITI proteins are involved in extracellular matrix stabilization and in the prevention of tumor metastasis. They are also structurally related plasma serine protease inhibitors and are composed of a light chain and varying numbers of heavy chains. This family member is thought to function as a tumor suppressor in breast and thyroid cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITIH5	NM_030569.7	c.2692G>C	p.Gly898Arg	missense_variant	Exon 14 of 14	ENST00000397146.7	NP_085046.5
ITIH5	NM_032817.6	c.2050G>C	p.Gly684Arg	missense_variant	Exon 10 of 10		NP_116206.4
ITIH5	XM_011519713.4	c.2767G>C	p.Gly923Arg	missense_variant	Exon 15 of 15		XP_011518015.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITIH5	ENST00000397146.7	c.2692G>C	p.Gly898Arg	missense_variant	Exon 14 of 14	1	NM_030569.7	ENSP00000380333.3
ITIH5	ENST00000613909.4	c.2050G>C	p.Gly684Arg	missense_variant	Exon 10 of 10	1		ENSP00000485414.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 22, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2692G>C (p.G898R) alteration is located in exon 14 (coding exon 14) of the ITIH5 gene. This alteration results from a G to C substitution at nucleotide position 2692, causing the glycine (G) at amino acid position 898 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.43
CADD	Uncertain	24
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.012	T;T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.062	D
MetaRNN	Uncertain	0.72	D;D
MetaSVM	Benign	-1.1	T
PrimateAI	Uncertain	0.51	T
Sift4G	Uncertain	0.0050	D;D
Vest4		0.63
MutPred		0.67		Gain of MoRF binding (P = 0.0222);.;
MVP		0.47
ClinPred		0.97	D
GERP RS		5.8
gMVP		0.77

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-7605183;