rs11698685

chr20-60320788-G-A

Variant summary

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

The NR_046099.1(MIR646HG):n.575G>A 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 0.302 in 152,048 control chromosomes in the GnomAD database, including 7,283 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 0.30 (7280 hom., cov: 32)
  • Exomes 𝑓: 0.25 (3 hom.)
• Consequence: MIR646HG NR_046099.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.575G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+139875G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45823 AN: 151872 Hom.: 7266 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.250 AC: 14 AN: 56 Hom.: 3 Cov.: 0 AF XY: 0.271 AC XY: 13 AN XY: 48

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.302 AC: 45872 AN: 151992 Hom.: 7280 Cov.: 32 AF XY: 0.300 AC XY: 22273 AN XY: 74284

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.305

Alfa AF: 0.309 Hom.: 1339

Bravo AF: 0.296

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11698685; hg19: chr20-58895846;