rs767649

chr21-25572410-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_001458.3(MIR155HG):n.199-1483T>A variant causes a intron, non coding transcript 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 NR_001458.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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=-0.67).
• 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/exons	MANE	UniProt
MIR155HG	NR_001458.3	n.199-1483T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR155HG	ENST00000456917.2	n.424-1483T>A		intron_variant, non_coding_transcript_variant		5
MIR155HG	ENST00000659862.2	n.296-1483T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0816

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.0760

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs767649; hg19: chr21-26944722;