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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369634	XR_931601.2	n.230G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR200CHG	ENST00000732834.1	n.847C>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000295827	ENST00000732905.1	n.241G>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000295827	ENST00000732907.1	n.191G>C		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs7305746; hg19: chr12-7072033;