rs1547354

Positions:

• chr21-25574397-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.703G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000456917.2	n.928G>A		non_coding_transcript_exon_variant	4/4	5
MIR155HG	ENST00000659862.2	n.800G>A		non_coding_transcript_exon_variant	3/3

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.200

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0357

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00158

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0726

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0470

Gnomad4 FIN AF: 0.00795

Gnomad4 NFE AF: 0.000882

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0200 Hom.: 17

Bravo AF: 0.0472

Asia WGS AF: 0.0980 AC: 339 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547354; hg19: chr21-26946709;