8-128150187-G-T

Position:

• chr8-128150187-G-T

Variant summary

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

The NR_031613.1(MIR1208):​n.72G>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 510,642 control chromosomes in the GnomAD database, including 5,359 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 0.11 (1250 hom., cov: 32)
  • Exomes 𝑓: 0.13 (4109 hom.)
• Consequence: MIR1208 NR_031613.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

MIR1208 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1208	NR_031613.1	n.72G>T		splice_region_variant, non_coding_transcript_exon_variant	1/1
MIR1208	unassigned_transcript_1536	n.*41G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1208	ENST00000408334.1	n.72G>T		splice_region_variant, non_coding_transcript_exon_variant	1/1	6
PVT1	ENST00000650846.1	n.403+2199G>T		intron_variant
PVT1	ENST00000651587.1	n.1378+2199G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16432 AN: 151982 Hom.: 1256 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.121

GnomAD3 exomes AF: 0.141 AC: 31193 AN: 220756 Hom.: 3306 AF XY: 0.137 AC XY: 16692 AN XY: 121546

Gnomad AFR exome AF: 0.0791

Gnomad AMR exome AF: 0.235

Gnomad ASJ exome AF: 0.0551

Gnomad EAS exome AF: 0.420

Gnomad SAS exome AF: 0.190

Gnomad FIN exome AF: 0.112

Gnomad NFE exome AF: 0.0852

Gnomad OTH exome AF: 0.112

GnomAD4 exome AF: 0.127 AC: 45365 AN: 358542 Hom.: 4109 Cov.: 0 AF XY: 0.129 AC XY: 26489 AN XY: 205748

Gnomad4 AFR exome AF: 0.0724

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.0557

Gnomad4 EAS exome AF: 0.419

Gnomad4 SAS exome AF: 0.186

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.0841

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.108 AC: 16433 AN: 152100 Hom.: 1250 Cov.: 32 AF XY: 0.114 AC XY: 8449 AN XY: 74342

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0477 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.81
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2648841; hg19: chr8-129162433;