rs56103835

Variant names:

• chr14-101056219-T-A
• rs56103835
• ENST00000385269.2:n.1T>A

Your query was ambiguous. Multiple possible variants found:

• chr14-101056219-T-A
• chr14-101056219-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000385269.2(MIR323B):​n.1T>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 0.00000263 in 380,768 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000026 (0 hom.)
• Consequence: MIR323B ENST00000385269.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 41 publications found

Genes affected

MIR323B (HGNC:38349): (microRNA 323b) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MEG9 (HGNC:43874): (maternally expressed 9)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR323B	NR_036133.1	n.1T>A		non_coding_transcript_exon_variant	Exon 1 of 1
MIR323B	unassigned_transcript_2435	n.-14T>A		upstream_gene_variant
MIR323B	unassigned_transcript_2436	n.-50T>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR323B	ENST00000385269.2	n.1T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
MEG9	ENST00000699460.1	n.2751T>A		non_coding_transcript_exon_variant	Exon 17 of 17
MEG9	ENST00000699461.1	n.356T>A		non_coding_transcript_exon_variant	Exon 3 of 7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000399 AC: 1 AN: 250342 AF XY: 0.00000738

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000263 AC: 1 AN: 380768 Hom.: 0 Cov.: 0 AF XY: 0.00000461 AC XY: 1 AN XY: 216880

African (AFR) AF: 0.00 AC: 0 AN: 10452

American (AMR) AF: 0.00 AC: 0 AN: 36276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11744

East Asian (EAS) AF: 0.00 AC: 0 AN: 13150

South Asian (SAS) AF: 0.0000150 AC: 1 AN: 66664

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32314

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1580

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 192004

Other (OTH) AF: 0.00 AC: 0 AN: 16584

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.2
DANN	Benign	0.85
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs56103835; hg19: chr14-101522556;