rs6854224

Variant names:

• chr4-183499719-C-T
• rs6854224
• ENST00000457303.4:n.320-2050G>A

Variant summary

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

The ENST00000457303.4(ING2-DT):​n.320-2050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,014 control chromosomes in the GnomAD database, including 17,676 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 0.45 (17676 hom., cov: 32)
• Consequence: ING2-DT ENST00000457303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 1 publications found

Genes affected

ING2-DT (HGNC:55723): (ING2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457303.4. 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-DT	NR_033995.2		n.341-2050G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ING2-DT	ENST00000457303.4	TSL:1	n.320-2050G>A		intron	N/A
	ING2-DT	ENST00000654924.2		n.539-2050G>A		intron	N/A
	ING2-DT	ENST00000736833.1		n.86-2050G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68222 AN: 151896 Hom.: 17675 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.449 AC: 68240 AN: 152014 Hom.: 17676 Cov.: 32 AF XY: 0.442 AC XY: 32845 AN XY: 74294

African (AFR) AF: 0.213 AC: 8841 AN: 41452

American (AMR) AF: 0.409 AC: 6241 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1772 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2045 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5590 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41457 AN: 67972

Other (OTH) AF: 0.469 AC: 989 AN: 2108

Alfa AF: 0.525 Hom.: 2822

Bravo AF: 0.425

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.48
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs6854224; hg19: chr4-184420872;