rs845787

Positions:

• chr20-26217295-C-T

Variant summary

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

The ENST00000670137.1(MIR663AHG):​n.250-25063G>A 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 0.482 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 ENST00000670137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

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 = 0.656 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.250-25063G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.479

Alfa AF: 0.425 Hom.: 19737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845787; hg19: chr20-26197931;