rs74057236

Variant names:

• chr12-6962550-G-A
• rs74057236
• ENST00000732834.1:n.527G>A

Variant summary

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

The ENST00000732834.1(MIR200CHG):​n.527G>A 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 0.0995 in 152,142 control chromosomes in the GnomAD database, including 899 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 0.10 (899 hom., cov: 33)
• Consequence: MIR200CHG ENST00000732834.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 6 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369634	XR_931601.2	n.550C>T		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.527G>A		non_coding_transcript_exon_variant	Exon 1 of 1
MIR200CHG	ENST00000732835.1	n.60G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000295827	ENST00000732907.1	n.511C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15128 AN: 152024 Hom.: 899 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0995 AC: 15145 AN: 152142 Hom.: 899 Cov.: 33 AF XY: 0.0961 AC XY: 7145 AN XY: 74378

African (AFR) AF: 0.153 AC: 6343 AN: 41494

American (AMR) AF: 0.0727 AC: 1111 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5166

South Asian (SAS) AF: 0.0680 AC: 328 AN: 4822

European-Finnish (FIN) AF: 0.0730 AC: 774 AN: 10596

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0905 AC: 6153 AN: 67984

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

Alfa AF: 0.0932 Hom.: 236

Bravo AF: 0.103

Asia WGS AF: 0.0440 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	18
DANN	Uncertain	0.98
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs74057236; hg19: chr12-7071713;