rs4817027

Variant names:

• chr21-25566677-G-A
• rs4817027
• ENST00000456917.2:n.339-3160G>A

Variant summary

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

The NR_001458.3(MIR155HG):​n.114-3160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,038 control chromosomes in the GnomAD database, including 28,752 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 0.59 (28752 hom., cov: 31)
• Consequence: MIR155HG NR_001458.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 8 publications found

Genes affected

MIR155HG (HGNC:35460): (MIR155 host gene) This gene represents a microRNA host gene. The long RNA transcribed from this gene is expressed at high levels in lymphoma and may function as an oncogene. [provided by RefSeq, Dec 2017]

ENSG00000229962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_001458.3. 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
	MIR155HG	NR_001458.3		n.114-3160G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR155HG	ENST00000456917.2	TSL:5	n.339-3160G>A		intron	N/A
	MIR155HG	ENST00000659862.3		n.434-3160G>A		intron	N/A
	ENSG00000229962	ENST00000779084.1		n.55+438C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88971 AN: 151920 Hom.: 28759 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.585 AC: 88970 AN: 152038 Hom.: 28752 Cov.: 31 AF XY: 0.577 AC XY: 42908 AN XY: 74324

African (AFR) AF: 0.355 AC: 14719 AN: 41436

American (AMR) AF: 0.540 AC: 8248 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2825 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5180

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4808

European-Finnish (FIN) AF: 0.699 AC: 7377 AN: 10554

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.743 AC: 50546 AN: 68002

Other (OTH) AF: 0.625 AC: 1321 AN: 2112

Alfa AF: 0.657 Hom.: 4685

Bravo AF: 0.566

Asia WGS AF: 0.308 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs4817027; hg19: chr21-26938989;