19-13836478-T-C

Position:

• chr19-13836478-T-C

Variant summary

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

The NR_029501.1(MIR27A):​n.40A>G 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 0.344 in 537,596 control chromosomes in the GnomAD database, including 32,640 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 0.37 (11005 hom., cov: 33)
  • Exomes 𝑓: 0.33 (21635 hom.)
• Consequence: MIR27A NR_029501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

MIR27A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR27A	NR_029501.1	n.40A>G		non_coding_transcript_exon_variant	1/1
MIR23AHG	NR_036515.2	n.6441A>G		non_coding_transcript_exon_variant	1/1
MIR27A	unassigned_transcript_3237	n.-11A>G		upstream_gene_variant
MIR27A	unassigned_transcript_3238	n.*9A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR27A	ENST00000385073.1	n.40A>G		non_coding_transcript_exon_variant	1/1	6
MIR23AHG	ENST00000587762.2	n.6451A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56711 AN: 151970 Hom.: 10988 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.319

GnomAD3 exomes AF: 0.335 AC: 81706 AN: 243584 Hom.: 13860 AF XY: 0.334 AC XY: 43985 AN XY: 131772

Gnomad AFR exome AF: 0.506

Gnomad AMR exome AF: 0.314

Gnomad ASJ exome AF: 0.272

Gnomad EAS exome AF: 0.277

Gnomad SAS exome AF: 0.346

Gnomad FIN exome AF: 0.362

Gnomad NFE exome AF: 0.326

Gnomad OTH exome AF: 0.319

GnomAD4 exome AF: 0.333 AC: 128355 AN: 385506 Hom.: 21635 Cov.: 0 AF XY: 0.333 AC XY: 72890 AN XY: 219050

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.312

Gnomad4 ASJ exome AF: 0.270

Gnomad4 EAS exome AF: 0.287

Gnomad4 SAS exome AF: 0.345

Gnomad4 FIN exome AF: 0.360

Gnomad4 NFE exome AF: 0.327

Gnomad4 OTH exome AF: 0.328

GnomAD4 genome AF: 0.373 AC: 56761 AN: 152090 Hom.: 11005 Cov.: 33 AF XY: 0.371 AC XY: 27595 AN XY: 74354

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.316

Alfa AF: 0.333 Hom.: 10455

Bravo AF: 0.373

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs895819; hg19: chr19-13947292; COSMIC: COSV54321327;