chr20-26217295-C-T

Variant names:

• chr20-26217295-C-T
• rs845787
• ENST00000594130.6:n.244-17772G>A

Variant summary

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

The ENST00000594130.6(MIR663AHG):​n.244-17772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,944 control chromosomes in the GnomAD database, including 18,894 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 0.48 (18894 hom., cov: 32)
• Consequence: MIR663AHG ENST00000594130.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 16 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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.244-17772G>A		intron_variant	Intron 1 of 3	5
MIR663AHG	ENST00000596767.6	n.205-17772G>A		intron_variant	Intron 1 of 5	5
MIR663AHG	ENST00000601119.6	n.265-17772G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73186 AN: 151826 Hom.: 18860 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.482 AC: 73261 AN: 151944 Hom.: 18894 Cov.: 32 AF XY: 0.477 AC XY: 35463 AN XY: 74268

African (AFR) AF: 0.663 AC: 27463 AN: 41450

American (AMR) AF: 0.512 AC: 7825 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1425 AN: 5158

South Asian (SAS) AF: 0.277 AC: 1334 AN: 4810

European-Finnish (FIN) AF: 0.421 AC: 4425 AN: 10522

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27911 AN: 67946

Other (OTH) AF: 0.479 AC: 1011 AN: 2112

Alfa AF: 0.432 Hom.: 27227

Bravo AF: 0.502

Asia WGS AF: 0.350 AC: 1217 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	0.77
DANN	Benign	0.57
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs845787; hg19: chr20-26197931;