rs7110670

Variant names:

• chr11-77986205-G-A
• rs7110670
• NM_033547.4:c.247-4629C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-77986205-G-A
• chr11-77986205-G-C

Variant summary

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

The NM_033547.4(INTS4):​c.247-4629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,126 control chromosomes in the GnomAD database, including 42,501 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 0.74 (42501 hom., cov: 32)
• Consequence: INTS4 NM_033547.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 9 publications found

Genes affected

INTS4 (HGNC:25048): (integrator complex subunit 4) INTS4 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033547.4. 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
	INTS4	NM_033547.4	MANE Select	c.247-4629C>T		intron	N/A	NP_291025.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS4	ENST00000534064.6	TSL:1 MANE Select	c.247-4629C>T		intron	N/A	ENSP00000434466.1
	INTS4	ENST00000529807.5	TSL:1	c.247-4629C>T		intron	N/A	ENSP00000433644.1
	INTS4	ENST00000433818.6	TSL:1	n.247-4629C>T		intron	N/A	ENSP00000407787.2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112912 AN: 152008 Hom.: 42457 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.743 AC: 113016 AN: 152126 Hom.: 42501 Cov.: 32 AF XY: 0.742 AC XY: 55185 AN XY: 74386

African (AFR) AF: 0.849 AC: 35229 AN: 41496

American (AMR) AF: 0.703 AC: 10748 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2571 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3754 AN: 5182

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4816

European-Finnish (FIN) AF: 0.797 AC: 8432 AN: 10584

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47657 AN: 67986

Other (OTH) AF: 0.727 AC: 1532 AN: 2106

Alfa AF: 0.705 Hom.: 12634

Bravo AF: 0.748

Asia WGS AF: 0.615 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7110670; hg19: chr11-77697251;