7-129770399-C-T

Position:

• chr7-129770399-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_029614.1(MIR182):​n.94G>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 0.0036 in 532,912 control chromosomes in the GnomAD database, including 11 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 0.0030 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0038 (9 hom.)
• Consequence: MIR182 NR_029614.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

MIR182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR182	NR_029614.1	n.94G>A		non_coding_transcript_exon_variant	1/1
MIR182	unassigned_transcript_1304	n.*7G>A		downstream_gene_variant
MIR182	unassigned_transcript_1305	n.*48G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR182	ENST00000385255.3	n.94G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000286380	ENST00000710872.1	n.432-6993G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00306 AC: 465 AN: 152182 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00460

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00345 AC: 864 AN: 250078 Hom.: 4 AF XY: 0.00373 AC XY: 505 AN XY: 135544

Gnomad AFR exome AF: 0.000807

Gnomad AMR exome AF: 0.00104

Gnomad ASJ exome AF: 0.00230

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00537

Gnomad FIN exome AF: 0.00102

Gnomad NFE exome AF: 0.00521

Gnomad OTH exome AF: 0.00294

GnomAD4 exome AF: 0.00383 AC: 1457 AN: 380612 Hom.: 9 Cov.: 0 AF XY: 0.00402 AC XY: 871 AN XY: 216616

Gnomad4 AFR exome AF: 0.000953

Gnomad4 AMR exome AF: 0.000966

Gnomad4 ASJ exome AF: 0.00222

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00543

Gnomad4 FIN exome AF: 0.00119

Gnomad4 NFE exome AF: 0.00486

Gnomad4 OTH exome AF: 0.00343

GnomAD4 genome AF: 0.00305 AC: 464 AN: 152300 Hom.: 2 Cov.: 32 AF XY: 0.00313 AC XY: 233 AN XY: 74466

Gnomad4 AFR AF: 0.00106

Gnomad4 AMR AF: 0.00333

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00459

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00398 Hom.: 2

Bravo AF: 0.00305

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs80041074; hg19: chr7-129410239;