rs2829801

Variant names:

• chr21-25571993-T-G
• rs2829801
• ENST00000456917.2:n.424-1900T>G

Variant summary

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

The ENST00000456917.2(MIR155HG):​n.424-1900T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,652 control chromosomes in the GnomAD database, including 31,156 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 0.62 (31156 hom., cov: 29)
• Consequence: MIR155HG ENST00000456917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.199-1900T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000456917.2	n.424-1900T>G		intron_variant	Intron 3 of 3	5
MIR155HG	ENST00000659862.3	n.519-1900T>G		intron_variant	Intron 2 of 2
MIR155HG	ENST00000779376.1	n.516-1900T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94273 AN: 151538 Hom.: 31157 Cov.: 29

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.622 AC: 94290 AN: 151652 Hom.: 31156 Cov.: 29 AF XY: 0.612 AC XY: 45354 AN XY: 74050

African (AFR) AF: 0.467 AC: 19313 AN: 41352

American (AMR) AF: 0.560 AC: 8522 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2829 AN: 3460

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5166

South Asian (SAS) AF: 0.438 AC: 2101 AN: 4802

European-Finnish (FIN) AF: 0.700 AC: 7314 AN: 10444

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 50990 AN: 67908

Other (OTH) AF: 0.660 AC: 1384 AN: 2098

Alfa AF: 0.725 Hom.: 17211

Bravo AF: 0.608

Asia WGS AF: 0.320 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs2829801; hg19: chr21-26944305;