rs7949144

Variant names:

• chr11-64890927-G-C
• rs7949144
• ENST00000413053.2:n.2280C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-64890927-G-C
• chr11-64890927-G-T

Variant summary

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

The ENST00000413053.2(MIR194-2HG):​n.2280C>G 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 0.0394 in 243,176 control chromosomes in the GnomAD database, including 300 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 0.040 (173 hom., cov: 31)
  • Exomes 𝑓: 0.039 (127 hom.)
• Consequence: MIR194-2HG ENST00000413053.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 3 publications found

Genes affected

MIR194-2HG (HGNC:51946): (MIR194-2 host gene)

MIR192 (HGNC:31562): (microRNA 192) 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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413053.2. 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
	MIR194-2HG	NR_133638.1		n.2280C>G		non_coding_transcript_exon	Exon 2 of 2
	MIR194-2HG	NR_133639.1		n.437+1502C>G		intron	N/A
	MIR194-2HG	NR_133640.1		n.277-1587C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR194-2HG	ENST00000413053.2	TSL:2	n.2280C>G		non_coding_transcript_exon	Exon 2 of 2
	MIR194-2HG	ENST00000710929.1		n.391-1587C>G		intron	N/A
	MIR194-2HG	ENST00000710930.1		n.551+1502C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6082 AN: 152132 Hom.: 173 Cov.: 31

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0469

GnomAD4 exome AF: 0.0386 AC: 3507 AN: 90926 Hom.: 127 Cov.: 0 AF XY: 0.0354 AC XY: 1791 AN XY: 50602

African (AFR) AF: 0.00783 AC: 9 AN: 1150

American (AMR) AF: 0.0293 AC: 113 AN: 3860

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 167 AN: 1736

East Asian (EAS) AF: 0.00 AC: 0 AN: 1250

South Asian (SAS) AF: 0.0144 AC: 313 AN: 21762

European-Finnish (FIN) AF: 0.0826 AC: 447 AN: 5412

Middle Eastern (MID) AF: 0.0765 AC: 26 AN: 340

European-Non Finnish (NFE) AF: 0.0434 AC: 2214 AN: 50984

Other (OTH) AF: 0.0492 AC: 218 AN: 4432

GnomAD4 genome AF: 0.0399 AC: 6081 AN: 152250 Hom.: 173 Cov.: 31 AF XY: 0.0413 AC XY: 3071 AN XY: 74430

African (AFR) AF: 0.0104 AC: 434 AN: 41540

American (AMR) AF: 0.0377 AC: 577 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0124 AC: 60 AN: 4834

European-Finnish (FIN) AF: 0.0948 AC: 1005 AN: 10604

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3486 AN: 68020

Other (OTH) AF: 0.0464 AC: 98 AN: 2110

Alfa AF: 0.0479 Hom.: 24

Bravo AF: 0.0351

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.0
DANN	Benign	0.69
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7949144; hg19: chr11-64658399;