rs2114358

Positions:

• chr8-128008933-G-A
• chr8-128008933-G-C

Variant summary

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

The NR_031611.1(MIR1206):​n.36G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 522,284 control chromosomes in the GnomAD database, including 101,439 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 0.65 (32173 hom., cov: 32)
  • Exomes 𝑓: 0.61 (69266 hom.)
• Consequence: MIR1206 NR_031611.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1206	NR_031611.1	n.36G>A		non_coding_transcript_exon_variant	1/1
PVT1	NR_003367.4	n.1221+19642G>A		intron_variant
PVT1	NR_186119.1	n.1585-657G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.971+19642G>A		intron_variant		1
MIR1206	ENST00000637127.1	n.36G>A		non_coding_transcript_exon_variant	1/1	6
PVT1	ENST00000653853.1	n.55G>A		non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98203 AN: 151886 Hom.: 32136 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.624

GnomAD3 exomes AF: 0.626 AC: 154054 AN: 246132 Hom.: 48779 AF XY: 0.616 AC XY: 82592 AN XY: 134010

Gnomad AFR exome AF: 0.731

Gnomad AMR exome AF: 0.697

Gnomad ASJ exome AF: 0.606

Gnomad EAS exome AF: 0.710

Gnomad SAS exome AF: 0.528

Gnomad FIN exome AF: 0.642

Gnomad NFE exome AF: 0.603

Gnomad OTH exome AF: 0.596

GnomAD4 exome AF: 0.608 AC: 225148 AN: 370280 Hom.: 69266 Cov.: 0 AF XY: 0.599 AC XY: 126400 AN XY: 211028

Gnomad4 AFR exome AF: 0.725

Gnomad4 AMR exome AF: 0.695

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.711

Gnomad4 SAS exome AF: 0.532

Gnomad4 FIN exome AF: 0.644

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.600

GnomAD4 genome AF: 0.647 AC: 98287 AN: 152004 Hom.: 32173 Cov.: 32 AF XY: 0.649 AC XY: 48231 AN XY: 74298

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.619

Alfa AF: 0.623 Hom.: 18721

Bravo AF: 0.657

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2114358; hg19: chr8-129021179;