12-26937617-A-C

Variant names:

• chr12-26937617-A-C
• rs2279351
• NM_018164.3:c.-12+179T>G

Variant summary

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

The NM_018164.3(INTS13):​c.-12+179T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,260 control chromosomes in the GnomAD database, including 1,618 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 (1618 hom., cov: 32)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: INTS13 NM_018164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 8 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS13	NM_018164.3	MANE Select	c.-12+179T>G		intron	N/A	NP_060634.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS13	ENST00000261191.12	TSL:1 MANE Select	c.-12+179T>G		intron	N/A	ENSP00000261191.7
	INTS13	ENST00000544548.5	TSL:3	c.-12+41T>G		intron	N/A	ENSP00000446183.1
	INTS13	ENST00000537336.1	TSL:3	c.-12+651T>G		intron	N/A	ENSP00000443066.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20942 AN: 152098 Hom.: 1611 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.182 AC: 8 AN: 44 Hom.: 0 Cov.: 0 AF XY: 0.206 AC XY: 7 AN XY: 34

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

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

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 8 AN: 40

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.138 AC: 20966 AN: 152216 Hom.: 1618 Cov.: 32 AF XY: 0.139 AC XY: 10352 AN XY: 74420

African (AFR) AF: 0.124 AC: 5142 AN: 41526

American (AMR) AF: 0.235 AC: 3602 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.0475 AC: 246 AN: 5182

South Asian (SAS) AF: 0.149 AC: 719 AN: 4828

European-Finnish (FIN) AF: 0.125 AC: 1325 AN: 10602

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

European-Non Finnish (NFE) AF: 0.134 AC: 9092 AN: 67998

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.135 Hom.: 6525

Bravo AF: 0.143

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.62
PhyloP100		1.5
PromoterAI		0.0098	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2279351; hg19: chr12-27090550;