rs2525720

Variant names:

• chr7-120964976-A-G
• rs2525720
• NM_019071.3:c.364+138A>G

Variant summary

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

The NM_019071.3(ING3):​c.364+138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 621,624 control chromosomes in the GnomAD database, including 18,334 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 0.28 (7123 hom., cov: 32)
  • Exomes 𝑓: 0.20 (11211 hom.)
• Consequence: ING3 NM_019071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019071.3. 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
	ING3	NM_019071.3	MANE Select	c.364+138A>G		intron	N/A	NP_061944.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ING3	ENST00000315870.10	TSL:1 MANE Select	c.364+138A>G		intron	N/A	ENSP00000320566.5	Q9NXR8-1
	ING3	ENST00000427726.5	TSL:1	n.268-1650A>G		intron	N/A	ENSP00000410406.1	Q9NXR8-3
	ING3	ENST00000875858.1		c.364+138A>G		intron	N/A	ENSP00000545917.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42019 AN: 151924 Hom.: 7102 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.0991

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.201 AC: 94505 AN: 469582 Hom.: 11211 AF XY: 0.195 AC XY: 48224 AN XY: 247846

African (AFR) AF: 0.464 AC: 6004 AN: 12926

American (AMR) AF: 0.144 AC: 2951 AN: 20508

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 2577 AN: 13962

East Asian (EAS) AF: 0.0505 AC: 1587 AN: 31418

South Asian (SAS) AF: 0.0990 AC: 4257 AN: 43004

European-Finnish (FIN) AF: 0.296 AC: 9725 AN: 32820

Middle Eastern (MID) AF: 0.166 AC: 599 AN: 3608

European-Non Finnish (NFE) AF: 0.215 AC: 61132 AN: 284780

Other (OTH) AF: 0.214 AC: 5673 AN: 26556

GnomAD4 genome AF: 0.277 AC: 42078 AN: 152042 Hom.: 7123 Cov.: 32 AF XY: 0.274 AC XY: 20341 AN XY: 74350

African (AFR) AF: 0.464 AC: 19237 AN: 41460

American (AMR) AF: 0.162 AC: 2477 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.0647 AC: 335 AN: 5178

South Asian (SAS) AF: 0.0980 AC: 473 AN: 4828

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14906 AN: 67946

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.274 Hom.: 884

Bravo AF: 0.274

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.078
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: rs2525720; hg19: chr7-120605030;