rs17801257

chr20-60317462-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.333-1459G>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 0.0987 in 152,250 control chromosomes in the GnomAD database, including 963 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 0.099 (963 hom., cov: 33)
• Consequence: MIR646HG NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.333-1459G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+136549G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0988 AC: 15025 AN: 152132 Hom.: 962 Cov.: 33

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.105

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0987 AC: 15030 AN: 152250 Hom.: 963 Cov.: 33 AF XY: 0.102 AC XY: 7572 AN XY: 74450

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0788

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.109

Alfa AF: 0.110 Hom.: 204

Bravo AF: 0.0841

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.29
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17801257; hg19: chr20-58892520;