12-26937997-G-GCACACACACACACACACACA

Position:

• chr12-26937997-G-GCACACACACACACACACACA

Variant summary

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

The ENST00000544548.5(INTS13):​c.-163-189_-163-188insTGTGTGTGTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000471 in 150,732 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00047 (1 hom., cov: 30)
• Consequence: INTS13 ENST00000544548.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

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]

INTS13 (HGNC:):

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/exons	MANE	Protein	UniProt
INTS13	NM_018164.3	c.-214_-213insTGTGTGTGTGTGTGTGTGTG		upstream_gene_variant		ENST00000261191.12	NP_060634.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INTS13	ENST00000544548.5	c.-163-189_-163-188insTGTGTGTGTGTGTGTGTGTG		intron_variant		3		ENSP00000446183.1
INTS13	ENST00000537336.1	c.-12+270_-12+271insTGTGTGTGTGTGTGTGTGTG		intron_variant		3		ENSP00000443066.1
INTS13	ENST00000261191.12	c.-214_-213insTGTGTGTGTGTGTGTGTGTG		upstream_gene_variant		1	NM_018164.3	ENSP00000261191.7
INTS13	ENST00000538727.5	c.-206_-205insTGTGTGTGTGTGTGTGTGTG		upstream_gene_variant		4		ENSP00000448467.1

Frequencies

GnomAD3 genomes AF: 0.000471 AC: 71 AN: 150618 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.00170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000664

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.000471 AC: 71 AN: 150732 Hom.: 1 Cov.: 30 AF XY: 0.000366 AC XY: 27 AN XY: 73688

Gnomad4 AFR AF: 0.00170

Gnomad4 AMR AF: 0.0000663

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149220083; hg19: chr12-27090930;