rs9375085

Variant names:

• chr6-98024688-G-C
• rs9375085
• ENST00000606913.5:n.156-74498G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-98024688-G-C
• chr6-98024688-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000607032.1(ENSG00000271860):​n.247-51379G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 169,920 control chromosomes in the GnomAD database, including 1,241 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 0.12 (1174 hom., cov: 32)
  • Exomes 𝑓: 0.092 (67 hom.)
• Consequence: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

ENSG00000271860 (HGNC:):

MIR2113 (HGNC:37058): (microRNA 2113) 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR2113	NR_031579.1	n.*67G>C		downstream_gene_variant
MIR2113	unassigned_transcript_1157	n.*82G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.156-74498G>C		intron_variant	Intron 1 of 4	5
ENSG00000271860	ENST00000607032.1	n.247-51379G>C		intron_variant	Intron 2 of 7	3
ENSG00000271860	ENST00000607823.5	n.267+55222G>C		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18174 AN: 151874 Hom.: 1172 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0935

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.0923 AC: 1655 AN: 17926 Hom.: 67 AF XY: 0.0941 AC XY: 807 AN XY: 8576

Gnomad4 AFR exome AF: 0.0750

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.0906

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.120 AC: 18176 AN: 151994 Hom.: 1174 Cov.: 32 AF XY: 0.120 AC XY: 8903 AN XY: 74292

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0567 Hom.: 67

Bravo AF: 0.129

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9375085; hg19: chr6-98472564; COSMIC: COSV71816442;