rs45547937

Positions:

• chr20-62564810-G-A

Variant summary

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

The NR_171007.1(MIR1-1HG):​n.788-179G>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 0.232 in 363,416 control chromosomes in the GnomAD database, including 10,295 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 0.25 (5181 hom., cov: 35)
  • Exomes 𝑓: 0.21 (5114 hom.)
• Consequence: MIR1-1HG NR_171007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

MIR1-1HG (HGNC:16159): (MIR1-1 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 (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1-1HG	NR_171007.1	n.788-179G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1-1HG	ENST00000624914.4	n.794-179G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38734 AN: 152046 Hom.: 5180 Cov.: 35

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.215 AC: 45409 AN: 211252 Hom.: 5114 AF XY: 0.211 AC XY: 24335 AN XY: 115092

Gnomad4 AFR exome AF: 0.343

Gnomad4 AMR exome AF: 0.239

Gnomad4 ASJ exome AF: 0.170

Gnomad4 EAS exome AF: 0.173

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.188

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.217

GnomAD4 genome AF: 0.255 AC: 38757 AN: 152164 Hom.: 5181 Cov.: 35 AF XY: 0.253 AC XY: 18823 AN XY: 74408

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.245

Alfa AF: 0.242 Hom.: 554

Bravo AF: 0.263

Asia WGS AF: 0.139 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	9.3
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: rs45547937; hg19: chr20-61162017; COSMIC: COSV61525825;