rs241202

Variant names:

• chr8-28776168-C-G
• rs241202
• NM_018250.4:c.1396-242G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-28776168-C-G
• chr8-28776168-C-T

Variant summary

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

The NM_018250.4(INTS9):​c.1396-242G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 412,902 control chromosomes in the GnomAD database, including 53,417 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 0.50 (19632 hom., cov: 32)
  • Exomes 𝑓: 0.50 (33785 hom.)
• Consequence: INTS9 NM_018250.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.30
• Publications: 6 publications found

Genes affected

INTS9 (HGNC:25592): (integrator complex subunit 9) This gene encodes a subunit of the Integrator complex. This protein complex binds the C-terminal domain of RNA polymerase II and likely plays a role in small nuclear RNA processing. The encoded protein has similarities to the subunits of the cleavage and polyadenylation specificity factor complex. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]

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 (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018250.4. 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
	INTS9	NM_018250.4	MANE Select	c.1396-242G>C		intron	N/A	NP_060720.2
	INTS9	NM_001363038.2		c.1396-242G>C		intron	N/A	NP_001349967.1
	INTS9	NM_001145159.3		c.1333-242G>C		intron	N/A	NP_001138631.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INTS9	ENST00000521022.6	TSL:1 MANE Select	c.1396-242G>C		intron	N/A	ENSP00000429065.1
	INTS9	ENST00000523303.5	TSL:1	n.1396-242G>C		intron	N/A	ENSP00000427952.1
	INTS9	ENST00000519578.1	TSL:3	n.36G>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76504 AN: 151932 Hom.: 19623 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.500 AC: 130459 AN: 260852 Hom.: 33785 Cov.: 2 AF XY: 0.500 AC XY: 66931 AN XY: 133764

African (AFR) AF: 0.517 AC: 3669 AN: 7100

American (AMR) AF: 0.477 AC: 4635 AN: 9714

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 4787 AN: 9270

East Asian (EAS) AF: 0.208 AC: 4449 AN: 21434

South Asian (SAS) AF: 0.408 AC: 4211 AN: 10326

European-Finnish (FIN) AF: 0.500 AC: 10021 AN: 20026

Middle Eastern (MID) AF: 0.515 AC: 670 AN: 1300

European-Non Finnish (NFE) AF: 0.543 AC: 89461 AN: 164814

Other (OTH) AF: 0.507 AC: 8556 AN: 16868

GnomAD4 genome AF: 0.503 AC: 76551 AN: 152050 Hom.: 19632 Cov.: 32 AF XY: 0.500 AC XY: 37167 AN XY: 74340

African (AFR) AF: 0.515 AC: 21349 AN: 41482

American (AMR) AF: 0.477 AC: 7297 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1042 AN: 5170

South Asian (SAS) AF: 0.370 AC: 1787 AN: 4826

European-Finnish (FIN) AF: 0.501 AC: 5287 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36333 AN: 67938

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.398 Hom.: 1130

Bravo AF: 0.506

Asia WGS AF: 0.320 AC: 1112 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	0.0020
DANN	Benign	0.49
PhyloP100		-6.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs241202; hg19: chr8-28633685;