chr4-183507591-A-G

Variant names:

• chr4-183507591-A-G
• rs4862213
• NM_001564.4:c.172+2224A>G

Variant summary

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

The NM_001564.4(ING2):​c.172+2224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,166 control chromosomes in the GnomAD database, including 3,194 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 0.18 (3194 hom., cov: 32)
• Consequence: ING2 NM_001564.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 4 publications found

Genes affected

ING2 (HGNC:6063): (inhibitor of growth family member 2) This gene is a member of the inhibitor of growth (ING) family. Members of the ING family associate with and modulate the activity of histone acetyltransferase (HAT) and histone deacetylase (HDAC) complexes and function in DNA repair and apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001564.4. 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
	ING2	NM_001564.4	MANE Select	c.172+2224A>G		intron	N/A	NP_001555.1	Q9H160-1
	ING2	NM_001291959.2		c.52+1273A>G		intron	N/A	NP_001278888.1	Q9H160-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ING2	ENST00000302327.4	TSL:1 MANE Select	c.172+2224A>G		intron	N/A	ENSP00000307183.3	Q9H160-1
	ING2	ENST00000412117.1	TSL:1	c.52+1273A>G		intron	N/A	ENSP00000410291.1	C9J4X5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27491 AN: 152048 Hom.: 3195 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.181 AC: 27496 AN: 152166 Hom.: 3194 Cov.: 32 AF XY: 0.174 AC XY: 12981 AN XY: 74404

African (AFR) AF: 0.0477 AC: 1980 AN: 41528

American (AMR) AF: 0.226 AC: 3450 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3466

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5184

South Asian (SAS) AF: 0.157 AC: 756 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17984 AN: 67988

Other (OTH) AF: 0.209 AC: 440 AN: 2102

Alfa AF: 0.239 Hom.: 5768

Bravo AF: 0.180

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.75
DANN	Benign	0.69
PhyloP100		-0.57
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: rs4862213; hg19: chr4-184428744;