rs1893650

Positions:

• chr21-25568503-T-C

Variant summary

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

The NR_001458.3(MIR155HG):​n.114-1334T>C 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 0.599 in 151,998 control chromosomes in the GnomAD database, including 29,659 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 0.60 (29659 hom., cov: 32)
• Consequence: MIR155HG NR_001458.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR155HG	NR_001458.3	n.114-1334T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR155HG	ENST00000456917.2	n.339-1334T>C		intron_variant, non_coding_transcript_variant		5
MIR155HG	ENST00000659862.2	n.211-1334T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91092 AN: 151880 Hom.: 29663 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.599 AC: 91099 AN: 151998 Hom.: 29659 Cov.: 32 AF XY: 0.590 AC XY: 43866 AN XY: 74310

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.637

Alfa AF: 0.716 Hom.: 75345

Bravo AF: 0.583

Asia WGS AF: 0.315 AC: 1100 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	6.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893650; hg19: chr21-26940815;