chr12-26937997-G-GCACACACACACACACA

Variant names:

• chr12-26937997-G-GCACACACACACACACA
• rs149220083
• ENST00000892608.1:c.-214_-213insTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000892608.1(INTS13):​c.-214_-213insTGTGTGTGTGTGTGTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00318 in 150,724 control chromosomes in the GnomAD database, including 3 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0032 (3 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: INTS13 ENST00000892608.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000892608.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS13	NM_018164.3	MANE Select	c.-214_-213insTGTGTGTGTGTGTGTG		upstream_gene	N/A	NP_060634.2	Q9NVM9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS13	ENST00000892608.1		c.-214_-213insTGTGTGTGTGTGTGTG		5_prime_UTR	Exon 1 of 17	ENSP00000562667.1
	INTS13	ENST00000892611.1		c.-214_-213insTGTGTGTGTGTGTGTG		5_prime_UTR	Exon 1 of 17	ENSP00000562670.1
	INTS13	ENST00000946631.1		c.-214_-213insTGTGTGTGTGTGTGTG		5_prime_UTR	Exon 1 of 17	ENSP00000616690.1

Frequencies

GnomAD3 genomes AF: 0.00315 AC: 475 AN: 150610 Hom.: 4 Cov.: 30

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000730

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: 0.0000149

Gnomad OTH AF: 0.00194

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 124

Other (OTH) AF: 0.00 AC: 0 AN: 10

GnomAD4 genome AF: 0.00318 AC: 480 AN: 150724 Hom.: 3 Cov.: 30 AF XY: 0.00315 AC XY: 232 AN XY: 73684

African (AFR) AF: 0.0112 AC: 464 AN: 41282

American (AMR) AF: 0.000729 AC: 11 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00 AC: 0 AN: 4698

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10480

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.0000149 AC: 1 AN: 67290

Other (OTH) AF: 0.00192 AC: 4 AN: 2082

Alfa AF: 0.00 Hom.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.34
Mutation Taster		=300/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs149220083; hg19: chr12-27090930;