rs731384

Positions:

• chr11-57640909-G-A

Variant summary

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

The ENST00000530595.1(MIR130AHG):​n.297+2237G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,024 control chromosomes in the GnomAD database, including 4,268 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 0.22 (4268 hom., cov: 32)
• Consequence: MIR130AHG ENST00000530595.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

MIR130AHG (HGNC:55966): (MIR130A host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR130AHG	ENST00000530595.1	n.297+2237G>A		intron_variant, non_coding_transcript_variant		2
MIR130AHG	ENST00000528466.1	n.155+2731G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33466 AN: 151906 Hom.: 4265 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33467 AN: 152024 Hom.: 4268 Cov.: 32 AF XY: 0.221 AC XY: 16408 AN XY: 74294

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.244

Alfa AF: 0.269 Hom.: 6197

Bravo AF: 0.203

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731384; hg19: chr11-57408382;