rs7305746

Variant names:

• chr12-6962870-C-G
• rs7305746
• ENST00000732834.1:n.847C>G

Your query was ambiguous. Multiple possible variants found:

• chr12-6962870-C-G
• chr12-6962870-C-T

Variant summary

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

The ENST00000732834.1(MIR200CHG):​n.847C>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 0.041 in 143,308 control chromosomes in the GnomAD database, including 386 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 0.041 (386 hom., cov: 33)
• Consequence: MIR200CHG ENST00000732834.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 0 publications found

Genes affected

MIR200CHG (HGNC:53161): (MIR200C and MIR141 host gene)

ENSG00000295827 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732834.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR200CHG	ENST00000732834.1		n.847C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295827	ENST00000732905.1		n.241G>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000295827	ENST00000732907.1		n.191G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 5852 AN: 143194 Hom.: 385 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000234

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00987

Gnomad NFE AF: 0.000597

Gnomad OTH AF: 0.0301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0410 AC: 5876 AN: 143308 Hom.: 386 Cov.: 33 AF XY: 0.0399 AC XY: 2775 AN XY: 69466

African (AFR) AF: 0.142 AC: 5501 AN: 38856

American (AMR) AF: 0.0195 AC: 276 AN: 14160

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3386

East Asian (EAS) AF: 0.00 AC: 0 AN: 4682

South Asian (SAS) AF: 0.000234 AC: 1 AN: 4274

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9592

Middle Eastern (MID) AF: 0.00709 AC: 2 AN: 282

European-Non Finnish (NFE) AF: 0.000597 AC: 39 AN: 65308

Other (OTH) AF: 0.0298 AC: 57 AN: 1912

Alfa AF: 0.00206 Hom.: 0

Bravo AF: 0.0450

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.9
DANN	Benign	0.84
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7305746;

hg19: chr12-7072033;