rs12483428

Variant names:

• chr21-25561470-T-C
• rs12483428
• ENST00000779476.1:n.743A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-25561470-T-C
• chr21-25561470-T-G

Variant summary

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

The ENST00000779476.1(ENSG00000301524):​n.743A>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 0.082 in 152,064 control chromosomes in the GnomAD database, including 1,291 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 0.082 (1291 hom., cov: 31)
• Consequence: ENSG00000301524 ENST00000779476.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 1 publications found

Genes affected

ENSG00000301524 (HGNC:):

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301524	ENST00000779476.1	n.743A>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000229962	ENST00000779084.1	n.55+5645A>G		intron_variant	Intron 1 of 4
MIR155HG	ENST00000779376.1	n.99-176T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12411 AN: 151946 Hom.: 1275 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.00792

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00127

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0820 AC: 12465 AN: 152064 Hom.: 1291 Cov.: 31 AF XY: 0.0814 AC XY: 6054 AN XY: 74362

African (AFR) AF: 0.229 AC: 9492 AN: 41446

American (AMR) AF: 0.108 AC: 1644 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3468

East Asian (EAS) AF: 0.153 AC: 790 AN: 5162

South Asian (SAS) AF: 0.0472 AC: 227 AN: 4808

European-Finnish (FIN) AF: 0.00792 AC: 84 AN: 10606

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.00127 AC: 86 AN: 67976

Other (OTH) AF: 0.0607 AC: 128 AN: 2110

Alfa AF: 0.0293 Hom.: 70

Bravo AF: 0.0973

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.45
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12483428; hg19: chr21-26933782;