chr21-25571713-A-G

Variant names:

• chr21-25571713-A-G
• rs928883
• ENST00000456917.2:n.423+1792A>G

Variant summary

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

The ENST00000456917.2(MIR155HG):​n.423+1792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,058 control chromosomes in the GnomAD database, including 53,112 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 0.83 (53112 hom., cov: 31)
• Consequence: MIR155HG ENST00000456917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 13 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]

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 = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.198+1792A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000456917.2	n.423+1792A>G		intron_variant	Intron 3 of 3	5
MIR155HG	ENST00000659862.3	n.518+1792A>G		intron_variant	Intron 2 of 2
MIR155HG	ENST00000779376.1	n.515+1792A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126447 AN: 151940 Hom.: 53067 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.832 AC: 126550 AN: 152058 Hom.: 53112 Cov.: 31 AF XY: 0.832 AC XY: 61820 AN XY: 74332

African (AFR) AF: 0.754 AC: 31255 AN: 41456

American (AMR) AF: 0.842 AC: 12863 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3247 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5158

South Asian (SAS) AF: 0.807 AC: 3887 AN: 4814

European-Finnish (FIN) AF: 0.879 AC: 9300 AN: 10586

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60059 AN: 67992

Other (OTH) AF: 0.849 AC: 1789 AN: 2106

Alfa AF: 0.853 Hom.: 7202

Bravo AF: 0.826

Asia WGS AF: 0.693 AC: 2413 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	3.1
DANN	Benign	0.77
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs928883; hg19: chr21-26944025;