rs767649

Variant names:

• chr21-25572410-T-A
• rs767649
• ENST00000456917.2:n.424-1483T>A

Variant summary

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

The ENST00000456917.2(MIR155HG):​n.424-1483T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 151,960 control chromosomes in the GnomAD database, including 826 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 0.080 (826 hom., cov: 32)
• Consequence: MIR155HG ENST00000456917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 56 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.199-1483T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000456917.2	n.424-1483T>A		intron_variant	Intron 3 of 3	5
MIR155HG	ENST00000659862.3	n.519-1483T>A		intron_variant	Intron 2 of 2
MIR155HG	ENST00000779376.1	n.516-1483T>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0800 AC: 12149 AN: 151842 Hom.: 828 Cov.: 32

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0799 AC: 12149 AN: 151960 Hom.: 826 Cov.: 32 AF XY: 0.0838 AC XY: 6222 AN XY: 74292

African (AFR) AF: 0.0471 AC: 1955 AN: 41520

American (AMR) AF: 0.110 AC: 1680 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1903 AN: 5174

South Asian (SAS) AF: 0.164 AC: 790 AN: 4810

European-Finnish (FIN) AF: 0.0816 AC: 853 AN: 10456

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4631 AN: 67958

Other (OTH) AF: 0.0760 AC: 160 AN: 2106

Alfa AF: 0.0675 Hom.: 56

Bravo AF: 0.0801

Asia WGS AF: 0.254 AC: 874 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs767649; hg19: chr21-26944722;