rs2525724

Variant names:

• chr7-120969889-A-G
• rs2525724
• NM_019071.3:c.908+685A>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.908+685A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,096 control chromosomes in the GnomAD database, including 7,117 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 (7117 hom., cov: 32)
• Consequence: ING3 NM_019071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• Publications: 3 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]

LOC124901734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ING3	NM_019071.3	c.908+685A>G		intron_variant	Intron 9 of 11	ENST00000315870.10	NP_061944.2
LOC124901734	XR_007060492.1	n.145+1312T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ING3	ENST00000315870.10	c.908+685A>G		intron_variant	Intron 9 of 11	1	NM_019071.3	ENSP00000320566.5
ING3	ENST00000427726.5	n.*529+685A>G		intron_variant	Intron 8 of 10	1		ENSP00000410406.1
ING3	ENST00000431467.1	c.863+685A>G		intron_variant	Intron 8 of 10	2		ENSP00000388506.1
ING3	ENST00000497502.1	n.505+685A>G		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42051 AN: 151978 Hom.: 7096 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.277 AC: 42110 AN: 152096 Hom.: 7117 Cov.: 32 AF XY: 0.274 AC XY: 20353 AN XY: 74364

African (AFR) AF: 0.464 AC: 19221 AN: 41452

American (AMR) AF: 0.162 AC: 2477 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.0647 AC: 336 AN: 5190

South Asian (SAS) AF: 0.107 AC: 516 AN: 4826

European-Finnish (FIN) AF: 0.309 AC: 3259 AN: 10562

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

European-Non Finnish (NFE) AF: 0.220 AC: 14928 AN: 67990

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.274 Hom.: 886

Bravo AF: 0.274

Asia WGS AF: 0.156 AC: 543 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.62
PhyloP100		0.66
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: rs2525724; hg19: chr7-120609943;