20-62554308-G-A

Position:

• chr20-62554308-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NR_029780.1(MIR1-1):​n.3G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00218 in 522,358 control chromosomes in the GnomAD database, including 9 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 0.0058 (9 hom., cov: 33)
  • Exomes 𝑓: 0.00069 (0 hom.)
• Consequence: MIR1-1 NR_029780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02

Genes affected

MIR1-1HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0058 (883/152324) while in subpopulation AFR AF= 0.0202 (840/41568). AF 95% confidence interval is 0.0191. There are 9 homozygotes in gnomad4. There are 404 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1-1	NR_029780.1	n.3G>A		non_coding_transcript_exon_variant	1/1
MIR1-1HG	NR_171007.1	n.787+643G>A		intron_variant
MIR1-1	unassigned_transcript_3476	n.-4G>A		upstream_gene_variant
MIR1-1	unassigned_transcript_3477	n.-43G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1-1HG	ENST00000624914.4	n.793+643G>A		intron_variant		1
MIR1-1	ENST00000362147.2	n.3G>A		non_coding_transcript_exon_variant	1/1	6
MIR1-1HG	ENST00000370523.3	n.241+643G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00576 AC: 877 AN: 152206 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.00148 AC: 371 AN: 250398 Hom.: 2 AF XY: 0.00105 AC XY: 142 AN XY: 135572

Gnomad AFR exome AF: 0.0201

Gnomad AMR exome AF: 0.000927

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000707

Gnomad OTH exome AF: 0.000982

GnomAD4 exome AF: 0.000689 AC: 255 AN: 370034 Hom.: 0 Cov.: 0 AF XY: 0.000463 AC XY: 97 AN XY: 209638

Gnomad4 AFR exome AF: 0.0197

Gnomad4 AMR exome AF: 0.000885

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000453

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000164

Gnomad4 OTH exome AF: 0.000806

GnomAD4 genome AF: 0.00580 AC: 883 AN: 152324 Hom.: 9 Cov.: 33 AF XY: 0.00542 AC XY: 404 AN XY: 74500

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.00242

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00192 Hom.: 1

Bravo AF: 0.00693

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6122014; hg19: chr20-61151515;