22-21653345-G-T

Position:

• chr22-21653345-G-T

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>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 0.00118 in 510,346 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 0.00092 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0013 (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=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR130B	NR_029845.1	n.42G>T		non_coding_transcript_exon_variant	1/1
LOC107985532	NR_169729.1	n.155G>T		non_coding_transcript_exon_variant	2/7
LOC107985532	NR_169730.1	n.155G>T		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>T		non_coding_transcript_exon_variant	1/1	6
ENSG00000207751	ENST00000498589.1	n.66G>T		non_coding_transcript_exon_variant	2/7	5
ENSG00000207751	ENST00000701182.1	n.152G>T		non_coding_transcript_exon_variant	2/4
ENSG00000207751	ENST00000701082.1	n.149-668G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.000920 AC: 140 AN: 152196 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000314

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00135

Gnomad OTH AF: 0.000958

GnomAD3 exomes AF: 0.00125 AC: 258 AN: 205910 Hom.: 0 AF XY: 0.00109 AC XY: 121 AN XY: 111196

Gnomad AFR exome AF: 0.000162

Gnomad AMR exome AF: 0.000679

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00211

Gnomad NFE exome AF: 0.00220

Gnomad OTH exome AF: 0.000579

GnomAD4 exome AF: 0.00129 AC: 463 AN: 358032 Hom.: 0 Cov.: 0 AF XY: 0.00108 AC XY: 220 AN XY: 203518

Gnomad4 AFR exome AF: 0.000100

Gnomad4 AMR exome AF: 0.000625

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00194

Gnomad4 NFE exome AF: 0.00199

Gnomad4 OTH exome AF: 0.00153

GnomAD4 genome AF: 0.000919 AC: 140 AN: 152314 Hom.: 0 Cov.: 33 AF XY: 0.000873 AC XY: 65 AN XY: 74470

Gnomad4 AFR AF: 0.000313

Gnomad4 AMR AF: 0.000457

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00135

Gnomad4 OTH AF: 0.000948

Alfa AF: 0.000747 Hom.: 0

Bravo AF: 0.00102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.83
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;