rs6513496

Positions:

• chr20-60308476-T-C

Variant summary

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

The NR_030376.1(MIR646):​n.3T>C 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 0.253 in 535,282 control chromosomes in the GnomAD database, including 18,707 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 0.28 (6675 hom., cov: 32)
  • Exomes 𝑓: 0.24 (12032 hom.)
• Consequence: MIR646 NR_030376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

Genes affected

MIR646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR646	NR_030376.1	n.3T>C		non_coding_transcript_exon_variant	1/1
MIR646HG	NR_046099.1	n.333-10445T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR646	ENST00000385067.1	n.3T>C		non_coding_transcript_exon_variant	1/1	6
MIR646HG	ENST00000421257.1	n.36-4834T>C		intron_variant		3
MIR646HG	ENST00000432910.5	n.333-10445T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42429 AN: 151766 Hom.: 6651 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.254

GnomAD3 exomes AF: 0.236 AC: 58464 AN: 248060 Hom.: 7589 AF XY: 0.239 AC XY: 32076 AN XY: 134474

Gnomad AFR exome AF: 0.425

Gnomad AMR exome AF: 0.144

Gnomad ASJ exome AF: 0.214

Gnomad EAS exome AF: 0.109

Gnomad SAS exome AF: 0.299

Gnomad FIN exome AF: 0.288

Gnomad NFE exome AF: 0.232

Gnomad OTH exome AF: 0.241

GnomAD4 exome AF: 0.242 AC: 92951 AN: 383398 Hom.: 12032 Cov.: 0 AF XY: 0.248 AC XY: 54139 AN XY: 218164

Gnomad4 AFR exome AF: 0.424

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.212

Gnomad4 EAS exome AF: 0.114

Gnomad4 SAS exome AF: 0.297

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.234

Gnomad4 OTH exome AF: 0.247

GnomAD4 genome AF: 0.280 AC: 42512 AN: 151884 Hom.: 6675 Cov.: 32 AF XY: 0.276 AC XY: 20495 AN XY: 74202

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.259

Alfa AF: 0.255 Hom.: 2363

Bravo AF: 0.274

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6513496; hg19: chr20-58883534;