rs6854224

Positions:

• chr4-183499719-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033995.2(ING2-DT):​n.341-2050G>A variant causes a intron, non coding transcript 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 NR_033995.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ING2-DT	NR_033995.2	n.341-2050G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ING2-DT	ENST00000457303.3	n.320-2050G>A		intron_variant, non_coding_transcript_variant		1
ING2-DT	ENST00000654924.1	n.535-2050G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.469

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6854224; hg19: chr4-184420872;