rs78054962

Positions:

• chr12-26938171-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000544548.5(INTS13):​c.-164+97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0058 in 152,634 control chromosomes in the GnomAD database, including 12 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 0.0057 (12 hom., cov: 32)
  • Exomes 𝑓: 0.023 (0 hom.)
• Consequence: INTS13 ENST00000544548.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00575 (874/152102) while in subpopulation EAS AF= 0.0345 (178/5160). AF 95% confidence interval is 0.0304. There are 12 homozygotes in gnomad4. There are 541 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INTS13	XM_011520750.3	c.-12+97A>G		intron_variant			XP_011519052.1
INTS13	XM_017019632.2	c.-12+97A>G		intron_variant			XP_016875121.1
INTS13	XM_017019635.2	c.-12+97A>G		intron_variant			XP_016875124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INTS13	ENST00000537336.1	c.-12+97A>G		intron_variant		3		ENSP00000443066
INTS13	ENST00000544548.5	c.-164+97A>G		intron_variant		3		ENSP00000446183

Frequencies

GnomAD3 genomes AF: 0.00576 AC: 875 AN: 151984 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00524

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00160

Gnomad OTH AF: 0.00527

GnomAD4 exome AF: 0.0226 AC: 12 AN: 532 Hom.: 0 Cov.: 0 AF XY: 0.0230 AC XY: 8 AN XY: 348

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0331

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00575 AC: 874 AN: 152102 Hom.: 12 Cov.: 32 AF XY: 0.00727 AC XY: 541 AN XY: 74370

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.00523

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.00416

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.00160

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.00410 Hom.: 2

Bravo AF: 0.00331

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs78054962; hg19: chr12-27091104;