15-89584309-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_152259.4(TICRR):c.958T>G(p.Trp320Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: TICRR NM_152259.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.81

Genes affected

TICRR (HGNC:28704): (TOPBP1 interacting checkpoint and replication regulator) Enables chromatin binding activity. Involved in regulation of DNA-dependent DNA replication initiation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.85

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TICRR	NM_152259.4	c.958T>G	p.Trp320Gly	missense_variant	3/22	ENST00000268138.12
TICRR	NM_001308025.1	c.955T>G	p.Trp319Gly	missense_variant	3/22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TICRR	ENST00000268138.12	c.958T>G	p.Trp320Gly	missense_variant	3/22	5	NM_152259.4	A2
TICRR	ENST00000560985.5	c.955T>G	p.Trp319Gly	missense_variant	3/22	1		P4
	ENST00000559041.1	n.48-7194T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 06, 2024

The c.958T>G (p.W320G) alteration is located in exon 3 (coding exon 3) of the TICRR gene. This alteration results from a T to G substitution at nucleotide position 958, causing the tryptophan (W) at amino acid position 320 to be replaced by a glycine (G). 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	0.37
BayesDel_addAF	Benign	-0.015	T
BayesDel_noAF	Benign	-0.26
Cadd	Uncertain	25
Dann	Uncertain	0.98
DEOGEN2	Benign	0.024	T;.
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.65	T;T
M_CAP	Benign	0.022	T
MetaRNN	Pathogenic	0.85	D;D
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.5	M;.
MutationTaster	Benign	0.51	D;D
PrimateAI	Benign	0.42	T
PROVEAN	Uncertain	-4.1	D;D
REVEL	Benign	0.18
Sift	Benign	0.030	D;D
Sift4G	Benign	0.097	T;T
Polyphen		0.99	D;.
Vest4		0.63
MutPred		0.69		Gain of disorder (P = 0.0042);.;
MVP		0.36
MPC		0.13
ClinPred		0.98	D
GERP RS		5.0
Varity_R		0.42
gMVP		0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr15-90127540;