20-26218217-C-A

Variant names:

• chr20-26218217-C-A
• rs845789
• ENST00000594130.6:n.244-18694G>T

Variant summary

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

The ENST00000594130.6(MIR663AHG):​n.244-18694G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,964 control chromosomes in the GnomAD database, including 11,218 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 0.31 (11218 hom., cov: 32)
• Consequence: MIR663AHG ENST00000594130.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

Genes affected

MIR663AHG (HGNC:27662): (MIR663A host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
MIR663AHG	ENST00000594130.6	n.244-18694G>T		intron_variant	Intron 1 of 3	5
MIR663AHG	ENST00000596767.6	n.205-18694G>T		intron_variant	Intron 1 of 5	5
MIR663AHG	ENST00000601119.6	n.265-18694G>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47409 AN: 151844 Hom.: 11198 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.312 AC: 47473 AN: 151964 Hom.: 11218 Cov.: 32 AF XY: 0.307 AC XY: 22825 AN XY: 74282

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.278

Alfa AF: 0.189 Hom.: 3239

Bravo AF: 0.338

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.38
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845789; hg19: chr20-26198853;