22-21653345-G-A

Position:

• chr22-21653345-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_029845.1(MIR130B):​n.42G>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 0.000611 in 510,358 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0015 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00024 (0 hom.)
• Consequence: MIR130B NR_029845.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75

Genes affected

MIR130B (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR130B	NR_029845.1	n.42G>A		non_coding_transcript_exon_variant	1/1
LOC107985532	NR_169729.1	n.155G>A		non_coding_transcript_exon_variant	2/7
LOC107985532	NR_169730.1	n.155G>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR130B	ENST00000385018.1	n.42G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000207751	ENST00000498589.1	n.66G>A		non_coding_transcript_exon_variant	2/7	5
ENSG00000207751	ENST00000701182.1	n.152G>A		non_coding_transcript_exon_variant	2/4
ENSG00000207751	ENST00000701082.1	n.149-668G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00149 AC: 227 AN: 152194 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00497

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.000408 AC: 84 AN: 205910 Hom.: 0 AF XY: 0.000333 AC XY: 37 AN XY: 111196

Gnomad AFR exome AF: 0.00501

Gnomad AMR exome AF: 0.000517

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000126

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000113

Gnomad OTH exome AF: 0.000579

GnomAD4 exome AF: 0.000237 AC: 85 AN: 358046 Hom.: 0 Cov.: 0 AF XY: 0.000187 AC XY: 38 AN XY: 203526

Gnomad4 AFR exome AF: 0.00450

Gnomad4 AMR exome AF: 0.000684

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000316

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000334

Gnomad4 OTH exome AF: 0.000448

GnomAD4 genome AF: 0.00149 AC: 227 AN: 152312 Hom.: 0 Cov.: 33 AF XY: 0.00125 AC XY: 93 AN XY: 74468

Gnomad4 AFR AF: 0.00496

Gnomad4 AMR AF: 0.00118

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.0000711 Hom.: 0

Bravo AF: 0.00168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.0
DANN	Benign	0.85
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: rs72631822; hg19: chr22-22007634;