rs11671784

Positions:

• chr19-13836482-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_029501.1(MIR27A):​n.36C>T 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 0.0123 in 539,264 control chromosomes in the GnomAD database, including 66 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 0.012 (18 hom., cov: 32)
  • Exomes 𝑓: 0.013 (48 hom.)
• Consequence: MIR27A NR_029501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948

Genes affected

MIR27A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0115 (1755/152338) while in subpopulation NFE AF= 0.0182 (1235/68024). AF 95% confidence interval is 0.0173. There are 18 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR27A	NR_029501.1	n.36C>T		non_coding_transcript_exon_variant	1/1
MIR23AHG	NR_036515.2	n.6437C>T		non_coding_transcript_exon_variant	1/1
MIR27A	unassigned_transcript_3237	n.-15C>T		upstream_gene_variant
MIR27A	unassigned_transcript_3238	n.*5C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR27A	ENST00000385073.1	n.36C>T		non_coding_transcript_exon_variant	1/1	6
MIR23AHG	ENST00000587762.2	n.6447C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1752 AN: 152222 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0177

GnomAD3 exomes AF: 0.0119 AC: 2918 AN: 245456 Hom.: 25 AF XY: 0.0121 AC XY: 1612 AN XY: 132826

Gnomad AFR exome AF: 0.00279

Gnomad AMR exome AF: 0.00867

Gnomad ASJ exome AF: 0.0337

Gnomad EAS exome AF: 0.0000551

Gnomad SAS exome AF: 0.00503

Gnomad FIN exome AF: 0.00214

Gnomad NFE exome AF: 0.0176

Gnomad OTH exome AF: 0.0168

GnomAD4 exome AF: 0.0126 AC: 4860 AN: 386926 Hom.: 48 Cov.: 0 AF XY: 0.0124 AC XY: 2719 AN XY: 219826

Gnomad4 AFR exome AF: 0.00263

Gnomad4 AMR exome AF: 0.00874

Gnomad4 ASJ exome AF: 0.0347

Gnomad4 EAS exome AF: 0.0000718

Gnomad4 SAS exome AF: 0.00544

Gnomad4 FIN exome AF: 0.00285

Gnomad4 NFE exome AF: 0.0171

Gnomad4 OTH exome AF: 0.0141

GnomAD4 genome AF: 0.0115 AC: 1755 AN: 152338 Hom.: 18 Cov.: 32 AF XY: 0.0110 AC XY: 821 AN XY: 74490

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00414

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0164 Hom.: 15

Bravo AF: 0.0118

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11671784; hg19: chr19-13947296;