chr5-143679868-T-C

Position:

• chr5-143679868-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR5197	NR_049829.1	n.9T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR5197	ENST00000583721.1	n.9T>C		non_coding_transcript_exon_variant	1/1
	ENST00000503323.1	n.379+7171T>C		intron_variant, non_coding_transcript_variant		3

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

GnomAD3 exomes AF: 0.219 AC: 14 AN: 64 Hom.: 1 AF XY: 0.156 AC XY: 5 AN XY: 32

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

Gnomad4 AFR exome AF: 0.394

Gnomad4 SAS exome AF: 0.314

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.401

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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.268

Alfa AF: 0.113 Hom.: 158

Bravo AF: 0.280

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2042253; hg19: chr5-143059433;