rs731384

Variant names:

• chr11-57640909-G-A
• rs731384
• ENST00000528466.1:n.155+2731G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528466.1(MIR130AHG):​n.155+2731G>A variant causes a intron 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 ENST00000528466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR130AHG	NR_186232.1	n.297+2237G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR130AHG	ENST00000528466.1	n.155+2731G>A		intron_variant	Intron 1 of 1	4
MIR130AHG	ENST00000530595.1	n.297+2237G>A		intron_variant	Intron 1 of 1	2
MIR130AHG	ENST00000815304.1	n.299+2237G>A		intron_variant	Intron 1 of 1
MIR130AHG	ENST00000815305.1	n.297+2237G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.106 AC: 4394 AN: 41492

American (AMR) AF: 0.190 AC: 2902 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1050 AN: 3472

East Asian (EAS) AF: 0.106 AC: 547 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1155 AN: 4802

European-Finnish (FIN) AF: 0.308 AC: 3248 AN: 10546

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19354 AN: 67960

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.263 Hom.: 8696

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs731384; hg19: chr11-57408382;