Variant chr12-26937997-G-GCA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000544548.5(INTS13):c.-163-190_-163-189dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 151,282 control chromosomes in the GnomAD database, including 439 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.075 ( 439 hom., cov: 30)

Exomes 𝑓: 0.035 ( 0 hom. )

Consequence

INTS13
ENST00000544548.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.339

Variant links:

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 links:

INTS13 (HGNC:):

INTS13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INTS13	NM_018164.3 linkuse as main transcript	c.-215_-214dupTG		upstream_gene_variant		ENST00000261191.12	NP_060634.2	Q9NVM9-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
INTS13	ENST00000544548.5 linkuse as main transcript	c.-163-190_-163-189dupTG	intron_variant	3		ENSP00000446183.1	F5H457
INTS13	ENST00000537336.1 linkuse as main transcript	c.-12+269_-12+270dupTG	intron_variant	3		ENSP00000443066.1	F5H5W1
INTS13	ENST00000261191.12 linkuse as main transcript	c.-215_-214dupTG	upstream_gene_variant	1	NM_018164.3	ENSP00000261191.7	Q9NVM9-1
INTS13	ENST00000538727.5 linkuse as main transcript	c.-207_-206dupTG	upstream_gene_variant	4		ENSP00000448467.1	F8VRX9

Frequencies

GnomAD3 genomes

AF:

0.0750

AC:

11298

AN:

150598

Hom.:

439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0744

Gnomad AMI

AF:

0.00221

Gnomad AMR

AF:

0.0765

Gnomad ASJ

AF:

0.0414

Gnomad EAS

AF:

0.0248

Gnomad SAS

AF:

0.0374

Gnomad FIN

AF:

0.0564

Gnomad MID

AF:

0.0484

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.0786

GnomAD4 exome

AF:

0.0351

AC:

AN:

570

Hom.:

Cov.:

AF XY:

0.0378

AC XY:

AN XY:

370

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0419

Gnomad4 NFE exome

AF:

0.0161

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0750

AC:

11300

AN:

150712

Hom.:

439

Cov.:

AF XY:

0.0731

AC XY:

5383

AN XY:

73680

show subpopulations

Gnomad4 AFR

AF:

0.0744

Gnomad4 AMR

AF:

0.0763

Gnomad4 ASJ

AF:

0.0414

Gnomad4 EAS

AF:

0.0248

Gnomad4 SAS

AF:

0.0368

Gnomad4 FIN

AF:

0.0564

Gnomad4 NFE

AF:

0.0872

Gnomad4 OTH

AF:

0.0783

Bravo

AF:

0.0748

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over