rs11844707

Variant names:

• chr14-101044276-G-A
• rs11844707
• ENST00000408687.1:n.79G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-101044276-G-A
• chr14-101044276-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000408687.1(MIR1185-2):​n.79G>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 0.0173 in 534,246 control chromosomes in the GnomAD database, including 649 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 0.045 (509 hom., cov: 33)
  • Exomes 𝑓: 0.0062 (140 hom.)
• Consequence: MIR1185-2 ENST00000408687.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 6 publications found

Genes affected

MIR1185-2 (HGNC:35254): (microRNA 1185-2) 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000408687.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1185-2	NR_031571.1		n.79G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1185-2	ENST00000408687.1	TSL:6	n.79G>A		non_coding_transcript_exon	Exon 1 of 1
	MEG9	ENST00000699460.1		n.627-45G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6871 AN: 152186 Hom.: 506 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0167

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000838

Gnomad OTH AF: 0.0315

GnomAD2 exomes AF: 0.0116 AC: 2857 AN: 245338 AF XY: 0.00877

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.00935

Gnomad ASJ exome AF: 0.00151

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000874

Gnomad OTH exome AF: 0.00597

GnomAD4 exome AF: 0.00618 AC: 2360 AN: 381942 Hom.: 140 Cov.: 0 AF XY: 0.00467 AC XY: 1016 AN XY: 217406

African (AFR) AF: 0.158 AC: 1655 AN: 10506

American (AMR) AF: 0.00965 AC: 350 AN: 36256

Ashkenazi Jewish (ASJ) AF: 0.00137 AC: 16 AN: 11694

East Asian (EAS) AF: 0.00 AC: 0 AN: 13176

South Asian (SAS) AF: 0.000315 AC: 21 AN: 66680

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32142

Middle Eastern (MID) AF: 0.0130 AC: 37 AN: 2854

European-Non Finnish (NFE) AF: 0.000630 AC: 121 AN: 191924

Other (OTH) AF: 0.00958 AC: 160 AN: 16710

GnomAD4 genome AF: 0.0452 AC: 6887 AN: 152304 Hom.: 509 Cov.: 33 AF XY: 0.0445 AC XY: 3311 AN XY: 74480

African (AFR) AF: 0.156 AC: 6498 AN: 41552

American (AMR) AF: 0.0167 AC: 255 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000838 AC: 57 AN: 68024

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0203 Hom.: 86

Bravo AF: 0.0511

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.89
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs11844707; hg19: chr14-101510613; COSMIC: COSV62999882;