20-60308547-T-G

Position:

• chr20-60308547-T-G

Variant summary

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

The NR_030376.1(MIR646):​n.74T>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 0.123 in 537,602 control chromosomes in the GnomAD database, including 6,402 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 0.17 (3629 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2773 hom.)
• Consequence: MIR646 NR_030376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

MIR646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR646	NR_030376.1	n.74T>G		non_coding_transcript_exon_variant	1/1
MIR646	unassigned_transcript_3469	n.14T>G		non_coding_transcript_exon_variant	1/1
MIR646HG	NR_046099.1	n.333-10374T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR646	ENST00000385067.1	n.74T>G		non_coding_transcript_exon_variant	1/1	6
MIR646HG	ENST00000421257.1	n.36-4763T>G		intron_variant		3
MIR646HG	ENST00000432910.5	n.333-10374T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25796 AN: 151922 Hom.: 3608 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.143

GnomAD3 exomes AF: 0.112 AC: 27823 AN: 248218 Hom.: 2350 AF XY: 0.109 AC XY: 14616 AN XY: 134598

Gnomad AFR exome AF: 0.390

Gnomad AMR exome AF: 0.0870

Gnomad ASJ exome AF: 0.0539

Gnomad EAS exome AF: 0.0982

Gnomad SAS exome AF: 0.144

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.0782

Gnomad OTH exome AF: 0.0981

GnomAD4 exome AF: 0.104 AC: 40089 AN: 385562 Hom.: 2773 Cov.: 0 AF XY: 0.105 AC XY: 23127 AN XY: 219362

Gnomad4 AFR exome AF: 0.388

Gnomad4 AMR exome AF: 0.0862

Gnomad4 ASJ exome AF: 0.0568

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.143

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.0788

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.170 AC: 25858 AN: 152040 Hom.: 3629 Cov.: 32 AF XY: 0.169 AC XY: 12546 AN XY: 74328

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0974 Hom.: 638

Bravo AF: 0.175

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6513497; hg19: chr20-58883605;