1-1312208-G-T

Position:

• chr1-1312208-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_017871.6(INTS11):​c.1607+18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (338 hom., cov: 20)
  • Exomes 𝑓: 0.033 (1778 hom.)
  • Failed GnomAD Quality Control
• Consequence: INTS11 NM_017871.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0330

Genes affected

INTS11 (HGNC:26052): (integrator complex subunit 11) The Integrator complex contains at least 12 subunits and associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates the 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690). INTS11, or CPSF3L, is the catalytic subunit of the Integrator complex (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 1-1312208-G-T is Benign according to our data. Variant chr1-1312208-G-T is described in ClinVar as [Benign]. Clinvar id is 1266568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INTS11	NM_017871.6	c.1607+18C>A		intron_variant		ENST00000435064.6	NP_060341.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INTS11	ENST00000435064.6	c.1607+18C>A		intron_variant		1	NM_017871.6	ENSP00000413493	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2067 AN: 117612 Hom.: 338 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.00408

Gnomad AMI AF: 0.00508

Gnomad AMR AF: 0.0117

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000804

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.00758

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0125

GnomAD3 exomes AF: 0.0254 AC: 2706 AN: 106506 Hom.: 381 AF XY: 0.0278 AC XY: 1566 AN XY: 56340

Gnomad AFR exome AF: 0.00460

Gnomad AMR exome AF: 0.00742

Gnomad ASJ exome AF: 0.0228

Gnomad EAS exome AF: 0.0000849

Gnomad SAS exome AF: 0.0385

Gnomad FIN exome AF: 0.0776

Gnomad NFE exome AF: 0.0367

Gnomad OTH exome AF: 0.0241

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0326 AC: 32777 AN: 1005634 Hom.: 1778 Cov.: 18 AF XY: 0.0327 AC XY: 16293 AN XY: 497644

Gnomad4 AFR exome AF: 0.00469

Gnomad4 AMR exome AF: 0.00796

Gnomad4 ASJ exome AF: 0.0241

Gnomad4 EAS exome AF: 0.0000308

Gnomad4 SAS exome AF: 0.0397

Gnomad4 FIN exome AF: 0.0575

Gnomad4 NFE exome AF: 0.0345

Gnomad4 OTH exome AF: 0.0324

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0175 AC: 2066 AN: 117752 Hom.: 338 Cov.: 20 AF XY: 0.0181 AC XY: 1033 AN XY: 57042

Gnomad4 AFR AF: 0.00407

Gnomad4 AMR AF: 0.0116

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.000804

Gnomad4 SAS AF: 0.0447

Gnomad4 FIN AF: 0.0338

Gnomad4 NFE AF: 0.0264

Gnomad4 OTH AF: 0.0124

Alfa AF: 0.00604 Hom.: 42

Bravo AF: 0.0135

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs568445177; hg19: chr1-1247588;