rs4817027

Positions:

• chr21-25566677-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.114-3160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,038 control chromosomes in the GnomAD database, including 28,752 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 0.59 (28752 hom., cov: 31)
• Consequence: MIR155HG NR_001458.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

MIR155HG (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR155HG	NR_001458.3	n.114-3160G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR155HG	ENST00000456917.2	n.339-3160G>A		intron_variant		5
MIR155HG	ENST00000659862.2	n.211-3160G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88971 AN: 151920 Hom.: 28759 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.585 AC: 88970 AN: 152038 Hom.: 28752 Cov.: 31 AF XY: 0.577 AC XY: 42908 AN XY: 74324

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.625

Alfa AF: 0.668 Hom.: 4635

Bravo AF: 0.566

Asia WGS AF: 0.308 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4817027; hg19: chr21-26938989;