12-6964642-G-T

Variant names:

• chr12-6964642-G-T
• rs16933011
• ENST00000537269.3:n.*184G>T

Variant summary

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

The ENST00000537269.3(MIR200CHG):​n.*184G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,160 control chromosomes in the GnomAD database, including 3,096 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 0.16 (3096 hom., cov: 33)
• Consequence: MIR200CHG ENST00000537269.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 7 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR200CHG	NR_135032.1	n.*195G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR200CHG	ENST00000537269.3	n.*184G>T		downstream_gene_variant		2
MIR200CHG	ENST00000732834.1	n.*184G>T		downstream_gene_variant
MIR200CHG	ENST00000732835.1	n.*195G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24006 AN: 152042 Hom.: 3083 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.158 AC: 24070 AN: 152160 Hom.: 3096 Cov.: 33 AF XY: 0.155 AC XY: 11530 AN XY: 74410

African (AFR) AF: 0.353 AC: 14625 AN: 41484

American (AMR) AF: 0.0956 AC: 1461 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5174

South Asian (SAS) AF: 0.0796 AC: 384 AN: 4826

European-Finnish (FIN) AF: 0.0734 AC: 778 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0885 AC: 6015 AN: 68004

Other (OTH) AF: 0.140 AC: 296 AN: 2112

Alfa AF: 0.111 Hom.: 1405

Bravo AF: 0.168

Asia WGS AF: 0.0920 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.052
DANN	Benign	0.74
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs16933011; hg19: chr12-7073805;