NM_016162.4:c.*268A>G

Variant names:

• chr12-6650927-T-C
• rs76290581
• NM_016162.4:c.*268A>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_016162.4(ING4):​c.*268A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 550,848 control chromosomes in the GnomAD database, including 5 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 0.0037 (2 hom., cov: 33)
  • Exomes 𝑓: 0.00043 (3 hom.)
• Consequence: ING4 NM_016162.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 4 publications found

Genes affected

ING4 (HGNC:19423): (inhibitor of growth family member 4) This gene encodes a tumor suppressor protein that contains a PHD-finger, which is a common motif in proteins involved in chromatin remodeling. This protein can bind TP53 and EP300/p300, a component of the histone acetyl transferase complex, suggesting its involvement in the TP53-dependent regulatory pathway. Multiple alternatively spliced transcript variants have been observed that encode distinct proteins. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ING4	NM_016162.4	c.*268A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000341550.9	NP_057246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ING4	ENST00000341550.9	c.*268A>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_016162.4	ENSP00000343396.4

Frequencies

GnomAD3 genomes AF: 0.00365 AC: 556 AN: 152200 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.000432 AC: 172 AN: 398530 Hom.: 3 Cov.: 0 AF XY: 0.000412 AC XY: 86 AN XY: 208746

African (AFR) AF: 0.0123 AC: 141 AN: 11450

American (AMR) AF: 0.000407 AC: 7 AN: 17208

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12420

East Asian (EAS) AF: 0.00 AC: 0 AN: 27796

South Asian (SAS) AF: 0.0000483 AC: 2 AN: 41374

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26006

Middle Eastern (MID) AF: 0.000571 AC: 1 AN: 1750

European-Non Finnish (NFE) AF: 0.0000169 AC: 4 AN: 237320

Other (OTH) AF: 0.000733 AC: 17 AN: 23206

GnomAD4 genome AF: 0.00365 AC: 556 AN: 152318 Hom.: 2 Cov.: 33 AF XY: 0.00320 AC XY: 238 AN XY: 74472

African (AFR) AF: 0.0131 AC: 544 AN: 41564

American (AMR) AF: 0.000588 AC: 9 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68020

Other (OTH) AF: 0.00142 AC: 3 AN: 2116

Alfa AF: 0.00169 Hom.: 1

Bravo AF: 0.00399

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		-0.49

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: rs76290581; hg19: chr12-6760093;