rs17485462

chr12-26932762-A-G

Variant summary

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

The NM_018164.3(INTS13):c.300+1794T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 149,672 control chromosomes in the GnomAD database, including 1,583 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 0.14 (1583 hom., cov: 32)
• Consequence: INTS13 NM_018164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

INTS13 (HGNC:20174): (integrator complex subunit 13) Involved in regulation of mitotic cell cycle. Acts upstream of or within centrosome localization; mitotic spindle organization; and protein localization to nuclear envelope. Located in cytoplasm and nuclear body. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INTS13	NM_018164.3	c.300+1794T>C		intron_variant		ENST00000261191.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INTS13	ENST00000261191.12	c.300+1794T>C		intron_variant		1	NM_018164.3	P1
INTS13	ENST00000537336.1	c.300+1794T>C		intron_variant		3
INTS13	ENST00000538727.5	c.-3-3857T>C		intron_variant		4
INTS13	ENST00000544548.5	c.300+1794T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 20765 AN: 149550 Hom.: 1576 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.139 AC: 20787 AN: 149672 Hom.: 1583 Cov.: 32 AF XY: 0.141 AC XY: 10283 AN XY: 73148

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.150

Alfa AF: 0.133 Hom.: 648

Bravo AF: 0.142

Asia WGS AF: 0.102 AC: 350 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.8
Dann	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs17485462; hg19: chr12-27085695;