rs41274312

Variant names:

• chr18-35904829-G-A
• rs41274312
• ENST00000385062.1:n.98C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-35904829-G-A
• chr18-35904829-G-C
• chr18-35904829-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NR_029616.1(MIR187):​n.98C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0134 in 492,798 control chromosomes in the GnomAD database, including 71 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 0.010 (12 hom., cov: 32)
  • Exomes 𝑓: 0.015 (59 hom.)
• Consequence: MIR187 NR_029616.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.17
• Publications: 9 publications found

Genes affected

MIR187 (HGNC:31558): (microRNA 187) 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]

ENSG00000300759 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0104 (1586/152300) while in subpopulation SAS AF = 0.0201 (97/4822). AF 95% confidence interval is 0.0169. There are 12 homozygotes in GnomAd4. There are 735 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_029616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR187	NR_029616.1		n.98C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR187	ENST00000385062.1	TSL:6	n.98C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000300759	ENST00000773858.1		n.252C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1587 AN: 152182 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00980

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0120

GnomAD2 exomes AF: 0.0120 AC: 2226 AN: 185376 AF XY: 0.0137

Gnomad AFR exome AF: 0.00270

Gnomad AMR exome AF: 0.00339

Gnomad ASJ exome AF: 0.00864

Gnomad EAS exome AF: 0.000431

Gnomad FIN exome AF: 0.0111

Gnomad NFE exome AF: 0.0155

Gnomad OTH exome AF: 0.0126

GnomAD4 exome AF: 0.0147 AC: 5021 AN: 340498 Hom.: 59 Cov.: 0 AF XY: 0.0158 AC XY: 3048 AN XY: 193174

African (AFR) AF: 0.00227 AC: 22 AN: 9672

American (AMR) AF: 0.00351 AC: 107 AN: 30462

Ashkenazi Jewish (ASJ) AF: 0.00804 AC: 88 AN: 10946

East Asian (EAS) AF: 0.000460 AC: 5 AN: 10874

South Asian (SAS) AF: 0.0235 AC: 1443 AN: 61288

European-Finnish (FIN) AF: 0.0108 AC: 302 AN: 27916

Middle Eastern (MID) AF: 0.0144 AC: 39 AN: 2716

European-Non Finnish (NFE) AF: 0.0163 AC: 2801 AN: 171504

Other (OTH) AF: 0.0142 AC: 214 AN: 15120

GnomAD4 genome AF: 0.0104 AC: 1586 AN: 152300 Hom.: 12 Cov.: 32 AF XY: 0.00987 AC XY: 735 AN XY: 74458

African (AFR) AF: 0.00255 AC: 106 AN: 41556

American (AMR) AF: 0.00588 AC: 90 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4822

European-Finnish (FIN) AF: 0.00980 AC: 104 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1127 AN: 68034

Other (OTH) AF: 0.0118 AC: 25 AN: 2112

Alfa AF: 0.0131 Hom.: 12

Bravo AF: 0.00929

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	22
DANN	Benign	0.95
PhyloP100		6.2

Splicing

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

Other links and lift over

dbSNP: rs41274312; hg19: chr18-33484792;