rs7938648

Variant names:

• chr11-77971836-A-C
• rs7938648
• NM_033547.4:c.471+7160T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-77971836-A-C
• chr11-77971836-A-G
• chr11-77971836-A-T

Variant summary

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

The NM_033547.4(INTS4):​c.471+7160T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 151,982 control chromosomes in the GnomAD database, including 44,263 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 0.76 (44263 hom., cov: 31)
• Consequence: INTS4 NM_033547.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 4 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 = 0.886 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS4	NM_033547.4	MANE Select	c.471+7160T>G		intron	N/A	NP_291025.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS4	ENST00000534064.6	TSL:1 MANE Select	c.471+7160T>G		intron	N/A	ENSP00000434466.1	Q96HW7-1
	INTS4	ENST00000529807.5	TSL:1	c.471+7160T>G		intron	N/A	ENSP00000433644.1	Q96HW7-2
	INTS4	ENST00000433818.6	TSL:1	n.364+9623T>G		intron	N/A	ENSP00000407787.2	F8WAA7

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114925 AN: 151864 Hom.: 44215 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.757 AC: 115035 AN: 151982 Hom.: 44263 Cov.: 31 AF XY: 0.755 AC XY: 56113 AN XY: 74280

African (AFR) AF: 0.894 AC: 37046 AN: 41454

American (AMR) AF: 0.710 AC: 10837 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2569 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3772 AN: 5182

South Asian (SAS) AF: 0.528 AC: 2541 AN: 4814

European-Finnish (FIN) AF: 0.798 AC: 8422 AN: 10560

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47673 AN: 67926

Other (OTH) AF: 0.739 AC: 1559 AN: 2110

Alfa AF: 0.637 Hom.: 1947

Bravo AF: 0.764

Asia WGS AF: 0.622 AC: 2166 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	1.2
DANN	Benign	0.18
PhyloP100		-0.99
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: rs7938648; hg19: chr11-77682882;