rs8032553

Variant names:

• chr15-89594094-A-G
• rs8032553
• NM_152259.4:c.1542-321A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-89594094-A-G
• chr15-89594094-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152259.4(TICRR):​c.1542-321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,086 control chromosomes in the GnomAD database, including 15,301 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 0.44 (15301 hom., cov: 32)
• Consequence: TICRR NM_152259.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TICRR	NM_152259.4	c.1542-321A>G		intron_variant	Intron 5 of 21	ENST00000268138.12	NP_689472.3
TICRR	NM_001308025.1	c.1539-321A>G		intron_variant	Intron 5 of 21		NP_001294954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TICRR	ENST00000268138.12	c.1542-321A>G		intron_variant	Intron 5 of 21	5	NM_152259.4	ENSP00000268138.7
TICRR	ENST00000560985.5	c.1539-321A>G		intron_variant	Intron 5 of 21	1		ENSP00000453306.1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66539 AN: 151970 Hom.: 15300 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.438 AC: 66561 AN: 152086 Hom.: 15301 Cov.: 32 AF XY: 0.438 AC XY: 32586 AN XY: 74360

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.437

Alfa AF: 0.493 Hom.: 30262

Bravo AF: 0.417

Asia WGS AF: 0.359 AC: 1250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.91

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: rs8032553; hg19: chr15-90137325;