20-60321657-A-G

Position:

• chr20-60321657-A-G

Variant summary

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

The NR_046099.1(MIR646HG):​n.1444A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,274 control chromosomes in the GnomAD database, including 12,892 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 0.40 (12892 hom., cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR646HG NR_046099.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

Genes affected

MIR646HG (HGNC:27659): (MIR646 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.1444A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+140744A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.397 AC: 59939 AN: 151158 Hom.: 12855 Cov.: 28

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.376

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.397 AC: 60034 AN: 151274 Hom.: 12892 Cov.: 28 AF XY: 0.391 AC XY: 28876 AN XY: 73906

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.380

Alfa AF: 0.359 Hom.: 7093

Bravo AF: 0.394

Asia WGS AF: 0.263 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6027506; hg19: chr20-58896715;