chr12-26937997-G-GCA

Variant names:

• chr12-26937997-G-GCA
• rs149220083
• ENST00000892608.1:c.-215_-214dupTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000892608.1(INTS13):​c.-215_-214dupTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 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 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

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.-215_-214dupTG		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.-215_-214dupTG		5_prime_UTR	Exon 1 of 17	ENSP00000562667.1
	INTS13	ENST00000892611.1		c.-215_-214dupTG		5_prime_UTR	Exon 1 of 17	ENSP00000562670.1
	INTS13	ENST00000946631.1		c.-215_-214dupTG		5_prime_UTR	Exon 1 of 17	ENSP00000616690.1

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11298 AN: 150598 Hom.: 439 Cov.: 30

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: 20 AN: 570 Hom.: 0 Cov.: 0 AF XY: 0.0378 AC XY: 14 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: 0.0419 AC: 18 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0161 AC: 2 AN: 124

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

GnomAD4 genome AF: 0.0750 AC: 11300 AN: 150712 Hom.: 439 Cov.: 30 AF XY: 0.0731 AC XY: 5383 AN XY: 73680

African (AFR) AF: 0.0744 AC: 3072 AN: 41284

American (AMR) AF: 0.0763 AC: 1151 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.0414 AC: 143 AN: 3454

East Asian (EAS) AF: 0.0248 AC: 128 AN: 5156

South Asian (SAS) AF: 0.0368 AC: 173 AN: 4698

European-Finnish (FIN) AF: 0.0564 AC: 591 AN: 10480

Middle Eastern (MID) AF: 0.0451 AC: 13 AN: 288

European-Non Finnish (NFE) AF: 0.0872 AC: 5864 AN: 67276

Other (OTH) AF: 0.0783 AC: 163 AN: 2082

Alfa AF: 0.0224 Hom.: 20

Bravo AF: 0.0748

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs149220083;

hg19: chr12-27090930;