rs17485462

Variant names:

• chr12-26932762-A-G
• rs17485462
• NM_018164.3:c.300+1794T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018164.3(INTS13):​c.300+1794T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 149,672 control chromosomes in the GnomAD database, including 1,583 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1583 hom., cov: 32)
• Consequence: INTS13 NM_018164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018164.3. 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.300+1794T>C		intron	N/A	NP_060634.2	Q9NVM9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS13	ENST00000261191.12	TSL:1 MANE Select	c.300+1794T>C		intron	N/A	ENSP00000261191.7	Q9NVM9-1
	INTS13	ENST00000892608.1		c.300+1794T>C		intron	N/A	ENSP00000562667.1
	INTS13	ENST00000892612.1		c.300+1794T>C		intron	N/A	ENSP00000562671.1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 20765 AN: 149550 Hom.: 1576 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.139 AC: 20787 AN: 149672 Hom.: 1583 Cov.: 32 AF XY: 0.141 AC XY: 10283 AN XY: 73148

African (AFR) AF: 0.124 AC: 5120 AN: 41416

American (AMR) AF: 0.237 AC: 3572 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 358 AN: 3410

East Asian (EAS) AF: 0.0499 AC: 249 AN: 4988

South Asian (SAS) AF: 0.146 AC: 699 AN: 4796

European-Finnish (FIN) AF: 0.128 AC: 1323 AN: 10336

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 8990 AN: 66410

Other (OTH) AF: 0.150 AC: 310 AN: 2070

Alfa AF: 0.133 Hom.: 727

Bravo AF: 0.142

Asia WGS AF: 0.102 AC: 350 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17485462; hg19: chr12-27085695;