rs2248890

Variant names:

• chr7-120957939-A-G
• rs2248890
• NM_019071.3:c.267+2315A>G

Variant summary

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

The ENST00000315870.10(ING3):​c.267+2315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,030 control chromosomes in the GnomAD database, including 14,731 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 0.39 (14731 hom., cov: 32)
• Consequence: ING3 ENST00000315870.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 1 publications found

Genes affected

ING3 (HGNC:14587): (inhibitor of growth family member 3) The protein encoded by this gene is similar to ING1, a tumor suppressor protein that can interact with TP53, inhibit cell growth, and induce apoptosis. This protein contains a PHD-finger, which is a common motif in proteins involved in chromatin remodeling. This gene can activate p53 trans-activated promoters, including promoters of p21/waf1 and bax. Overexpression of this gene has been shown to inhibit cell growth and induce apoptosis. Allelic loss and reduced expression of this gene were detected in head and neck cancers. Two alternatively spliced transcript variants encoding different isoforms have been observed. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000315870.10. 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
	ING3	NM_019071.3	MANE Select	c.267+2315A>G		intron	N/A	NP_061944.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ING3	ENST00000315870.10	TSL:1 MANE Select	c.267+2315A>G		intron	N/A	ENSP00000320566.5
	ING3	ENST00000427726.5	TSL:1	n.267+2315A>G		intron	N/A	ENSP00000410406.1
	ING3	ENST00000431467.1	TSL:2	c.222+2315A>G		intron	N/A	ENSP00000388506.1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59768 AN: 151912 Hom.: 14672 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.394 AC: 59899 AN: 152030 Hom.: 14731 Cov.: 32 AF XY: 0.396 AC XY: 29444 AN XY: 74316

African (AFR) AF: 0.696 AC: 28862 AN: 41468

American (AMR) AF: 0.347 AC: 5313 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1901 AN: 5160

South Asian (SAS) AF: 0.241 AC: 1163 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4253 AN: 10534

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16666 AN: 67968

Other (OTH) AF: 0.350 AC: 740 AN: 2112

Alfa AF: 0.336 Hom.: 1320

Bravo AF: 0.408

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.0
DANN	Benign	0.71
PhyloP100		0.31
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: rs2248890; hg19: chr7-120597993;