rs845789

Positions:

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

Variant summary

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

The ENST00000670137.1(MIR663AHG):​n.250-25985G>T 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 0.312 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 ENST00000670137.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR663AHG	ENST00000670137.1	n.250-25985G>T		intron_variant, non_coding_transcript_variant

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;