rs845789

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-26218217-C-A
• chr20-26218217-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000300939 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.663 AC: 27467 AN: 41410

American (AMR) AF: 0.287 AC: 4387 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3468

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5176

South Asian (SAS) AF: 0.163 AC: 785 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10556

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11356 AN: 67956

Other (OTH) AF: 0.278 AC: 587 AN: 2110

Alfa AF: 0.197 Hom.: 4259

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
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs845789; hg19: chr20-26198853;