NM_001564.4:c.173-1776G>A

Variant names:

• chr4-183508506-G-A
• rs6830958
• NM_001564.4:c.173-1776G>A

Variant summary

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

The NM_001564.4(ING2):​c.173-1776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,070 control chromosomes in the GnomAD database, including 41,531 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 0.74 (41531 hom., cov: 32)
• Consequence: ING2 NM_001564.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ING2	NM_001564.4	c.173-1776G>A		intron_variant	Intron 1 of 1	ENST00000302327.4	NP_001555.1
ING2	NM_001291959.2	c.53-1776G>A		intron_variant	Intron 1 of 1		NP_001278888.1
ING2	XM_011531927.3	c.7+1489G>A		intron_variant	Intron 1 of 1		XP_011530229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ING2	ENST00000302327.4	c.173-1776G>A		intron_variant	Intron 1 of 1	1	NM_001564.4	ENSP00000307183.3
ING2	ENST00000412117.1	c.53-1776G>A		intron_variant	Intron 1 of 1	1		ENSP00000410291.1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111732 AN: 151952 Hom.: 41495 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.735 AC: 111830 AN: 152070 Hom.: 41531 Cov.: 32 AF XY: 0.732 AC XY: 54436 AN XY: 74342

African (AFR) AF: 0.707 AC: 29329 AN: 41456

American (AMR) AF: 0.635 AC: 9709 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2383 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3093 AN: 5168

South Asian (SAS) AF: 0.637 AC: 3070 AN: 4822

European-Finnish (FIN) AF: 0.814 AC: 8623 AN: 10588

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53343 AN: 67978

Other (OTH) AF: 0.716 AC: 1507 AN: 2106

Alfa AF: 0.756 Hom.: 103265

Bravo AF: 0.719

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.50
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.20		Position offset: -3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6830958; hg19: chr4-184429659;