dbSNP rs2525720: ING3:c.364+138A>G (chr7-120964976-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0780

Publications

1 publications found

Variant links:

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]

ING3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ING3	NM_019071.3 link	c.364+138A>G		intron_variant	Intron 5 of 11	ENST00000315870.10	NP_061944.2
ING3	XM_047420535.1 link	c.268-1650A>G		intron_variant	Intron 4 of 4		XP_047276491.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ING3	ENST00000315870.10 link	c.364+138A>G	intron_variant	Intron 5 of 11	1	NM_019071.3	ENSP00000320566.5
ING3	ENST00000427726.5 link	n.268-1650A>G	intron_variant	Intron 4 of 10	1		ENSP00000410406.1
ING3	ENST00000431467.1 link	c.319+138A>G	intron_variant	Intron 4 of 10	2		ENSP00000388506.1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42019

AN:

151924

Hom.:

7102

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3440

6881

10321

13762

17202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

496

992

1488

1984

2480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.277

AC:

42078

AN:

152042

Hom.:

7123

Cov.:

AF XY:

0.274

AC XY:

20341

AN XY:

74350

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14906

AN:

67946

Other (OTH)

AF:

0.241

AC:

510

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1433

2866

4299

5732

7165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.078

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over