chr12-26937997-G-GCACACACA

Position:

• chr12-26937997-G-GCACACACA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000544548.5(INTS13):​c.-163-196_-163-189dupTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00995 in 150,724 control chromosomes in the GnomAD database, including 26 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.010 (26 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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 Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00995 (1500/150724) while in subpopulation AFR AF= 0.0341 (1409/41282). AF 95% confidence interval is 0.0326. There are 26 homozygotes in gnomad4. There are 657 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INTS13	NM_018164.3	c.-221_-214dupTGTGTGTG		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.-163-196_-163-189dupTGTGTGTG		intron_variant		3		ENSP00000446183.1
INTS13	ENST00000537336.1	c.-12+263_-12+270dupTGTGTGTG		intron_variant		3		ENSP00000443066.1
INTS13	ENST00000261191.12	c.-221_-214dupTGTGTGTG		upstream_gene_variant		1	NM_018164.3	ENSP00000261191.7
INTS13	ENST00000538727.5	c.-213_-206dupTGTGTGTG		upstream_gene_variant		4		ENSP00000448467.1

Frequencies

GnomAD3 genomes AF: 0.00994 AC: 1497 AN: 150610 Hom.: 26 Cov.: 30

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00425

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000213

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000163

Gnomad OTH AF: 0.00728

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 570 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 370

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00995 AC: 1500 AN: 150724 Hom.: 26 Cov.: 30 AF XY: 0.00892 AC XY: 657 AN XY: 73684

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.00424

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000213

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000163

Gnomad4 OTH AF: 0.00720

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;