rs1547354

Variant names:

• chr21-25574397-G-A
• rs1547354
• ENST00000456917.2:n.928G>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.703G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 152,980 control chromosomes in the GnomAD database, including 259 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 0.037 (258 hom., cov: 33)
  • Exomes 𝑓: 0.0066 (1 hom.)
• Consequence: MIR155HG NR_001458.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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.703G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR155HG	ENST00000456917.2	TSL:5	n.928G>A		non_coding_transcript_exon	Exon 4 of 4
	MIR155HG	ENST00000659862.3		n.1023G>A		non_coding_transcript_exon	Exon 3 of 3
	MIR155HG	ENST00000779376.1		n.1020G>A		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0370 AC: 5618 AN: 151958 Hom.: 258 Cov.: 33

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0469

Gnomad FIN AF: 0.00795

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.0312

GnomAD4 exome AF: 0.00664 AC: 6 AN: 904 Hom.: 1 Cov.: 0 AF XY: 0.0107 AC XY: 5 AN XY: 468

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.200 AC: 2 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.0357 AC: 3 AN: 84

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 60

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.00158 AC: 1 AN: 634

Other (OTH) AF: 0.00 AC: 0 AN: 88

GnomAD4 genome AF: 0.0370 AC: 5625 AN: 152076 Hom.: 258 Cov.: 33 AF XY: 0.0385 AC XY: 2862 AN XY: 74322

African (AFR) AF: 0.0726 AC: 3011 AN: 41446

American (AMR) AF: 0.0903 AC: 1379 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.153 AC: 795 AN: 5184

South Asian (SAS) AF: 0.0470 AC: 226 AN: 4810

European-Finnish (FIN) AF: 0.00795 AC: 84 AN: 10566

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000882 AC: 60 AN: 68010

Other (OTH) AF: 0.0313 AC: 66 AN: 2108

Alfa AF: 0.0174 Hom.: 54

Bravo AF: 0.0472

Asia WGS AF: 0.0980 AC: 339 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.59
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1547354; hg19: chr21-26946709;