chr8-128150187-G-A

Position:

• chr8-128150187-G-A

Variant summary

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

The NR_031613.1(MIR1208):​n.72G>A 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 0.0417 in 510,780 control chromosomes in the GnomAD database, including 726 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 0.048 (267 hom., cov: 32)
  • Exomes 𝑓: 0.039 (459 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 (AFR) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7263 AN: 152004 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0407

GnomAD3 exomes AF: 0.0422 AC: 9315 AN: 220756 Hom.: 299 AF XY: 0.0420 AC XY: 5100 AN XY: 121546

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.0689

Gnomad ASJ exome AF: 0.0422

Gnomad EAS exome AF: 0.0516

Gnomad SAS exome AF: 0.0764

Gnomad FIN exome AF: 0.0253

Gnomad NFE exome AF: 0.0197

Gnomad OTH exome AF: 0.0430

GnomAD4 exome AF: 0.0391 AC: 14020 AN: 358658 Hom.: 459 Cov.: 0 AF XY: 0.0410 AC XY: 8442 AN XY: 205804

Gnomad4 AFR exome AF: 0.0989

Gnomad4 AMR exome AF: 0.0679

Gnomad4 ASJ exome AF: 0.0420

Gnomad4 EAS exome AF: 0.0586

Gnomad4 SAS exome AF: 0.0753

Gnomad4 FIN exome AF: 0.0257

Gnomad4 NFE exome AF: 0.0199

Gnomad4 OTH exome AF: 0.0366

GnomAD4 genome AF: 0.0480 AC: 7299 AN: 152122 Hom.: 267 Cov.: 32 AF XY: 0.0478 AC XY: 3554 AN XY: 74358

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.0543

Gnomad4 SAS AF: 0.0717

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0408

Alfa AF: 0.0180 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	5.1
DANN	Benign	0.49

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;