5-143679868-T-C

Variant names:

• chr5-143679868-T-C
• rs2042253
• ENST00000583721.1:n.9T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_049829.1(MIR5197):​n.9T>C 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 0.269 in 154,056 control chromosomes in the GnomAD database, including 5,817 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 0.27 (5682 hom., cov: 32)
  • Exomes 𝑓: 0.36 (135 hom.)
• Consequence: MIR5197 NR_049829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 19 publications found

Genes affected

MIR5197 (HGNC:43450): (microRNA 5197) 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]

ENSG00000249881 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_049829.1. 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
	MIR5197	NR_049829.1		n.9T>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR5197	ENST00000583721.1	TSL:6	n.9T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000249881	ENST00000503323.1	TSL:3	n.379+7171T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40757 AN: 151976 Hom.: 5672 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.267

GnomAD2 exomes AF: 0.219 AC: 14 AN: 64 AF XY: 0.156

Gnomad AFR exome AF: 0.250

Gnomad ASJ exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.231

Gnomad OTH exome AF: 0.250

GnomAD4 exome AF: 0.360 AC: 706 AN: 1962 Hom.: 135 Cov.: 0 AF XY: 0.365 AC XY: 360 AN XY: 986

African (AFR) AF: 0.394 AC: 26 AN: 66

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.314 AC: 27 AN: 86

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.357 AC: 580 AN: 1626

European-Non Finnish (NFE) AF: 0.400 AC: 4 AN: 10

Other (OTH) AF: 0.401 AC: 69 AN: 172

GnomAD4 genome AF: 0.268 AC: 40800 AN: 152094 Hom.: 5682 Cov.: 32 AF XY: 0.267 AC XY: 19884 AN XY: 74370

African (AFR) AF: 0.321 AC: 13324 AN: 41492

American (AMR) AF: 0.253 AC: 3865 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1963 AN: 5158

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4814

European-Finnish (FIN) AF: 0.157 AC: 1658 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16361 AN: 67982

Other (OTH) AF: 0.268 AC: 565 AN: 2112

Alfa AF: 0.124 Hom.: 193

Bravo AF: 0.280

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2042253; hg19: chr5-143059433;