rs845785

chr20-26213468-G-A

Variant summary

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

The ENST00000670137.1(MIR663AHG):n.250-21236C>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 0.32 in 152,046 control chromosomes in the GnomAD database, including 11,917 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 0.32 (11917 hom., cov: 32)
• Consequence: MIR663AHG ENST00000670137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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.250-21236C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48535 AN: 151928 Hom.: 11891 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.320 AC: 48606 AN: 152046 Hom.: 11917 Cov.: 32 AF XY: 0.314 AC XY: 23359 AN XY: 74338

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.286

Alfa AF: 0.184 Hom.: 7017

Bravo AF: 0.347

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845785; hg19: chr20-26194104;