chr21-25565010-C-G

Variant names:

• chr21-25565010-C-G
• rs987195
• ENST00000779380.1:n.256C>G

Variant summary

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

The ENST00000779380.1(MIR155HG):​n.256C>G 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 0.0799 in 152,204 control chromosomes in the GnomAD database, including 824 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 (824 hom., cov: 32)
• Consequence: MIR155HG ENST00000779380.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 7 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]

ENSG00000229962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.113+2753C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000779380.1	n.256C>G		non_coding_transcript_exon_variant	Exon 3 of 5
MIR155HG	ENST00000456917.2	n.338+2753C>G		intron_variant	Intron 2 of 3	5
MIR155HG	ENST00000659862.3	n.433+2753C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0800 AC: 12162 AN: 152086 Hom.: 826 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0799 AC: 12162 AN: 152204 Hom.: 824 Cov.: 32 AF XY: 0.0836 AC XY: 6222 AN XY: 74416

African (AFR) AF: 0.0472 AC: 1961 AN: 41542

American (AMR) AF: 0.110 AC: 1683 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1896 AN: 5166

South Asian (SAS) AF: 0.164 AC: 789 AN: 4820

European-Finnish (FIN) AF: 0.0814 AC: 862 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0681 AC: 4633 AN: 68006

Other (OTH) AF: 0.0762 AC: 161 AN: 2112

Alfa AF: 0.0161 Hom.: 13

Bravo AF: 0.0802

Asia WGS AF: 0.253 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs987195; hg19: chr21-26937322;