rs12135382

Variant names:

• chr1-1163041-C-T
• rs12135382
• XR_007065348.1:n.165C>T

Variant summary

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

The XR_007065348.1(MIR200BHG):​n.165C>T 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 0.472 in 152,216 control chromosomes in the GnomAD database, including 18,607 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 0.47 (18607 hom., cov: 36)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 3 publications found

Genes affected

MIR200BHG (HGNC:58145):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR200BHG	XR_007065348.1	n.165C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71807 AN: 152098 Hom.: 18601 Cov.: 36

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.472 AC: 71833 AN: 152216 Hom.: 18607 Cov.: 36 AF XY: 0.467 AC XY: 34797 AN XY: 74436

African (AFR) AF: 0.269 AC: 11176 AN: 41528

American (AMR) AF: 0.627 AC: 9593 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1456 AN: 5162

South Asian (SAS) AF: 0.455 AC: 2197 AN: 4828

European-Finnish (FIN) AF: 0.471 AC: 4989 AN: 10598

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38611 AN: 68004

Other (OTH) AF: 0.498 AC: 1053 AN: 2116

Alfa AF: 0.517 Hom.: 3269

Bravo AF: 0.475

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.79
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12135382; hg19: chr1-1098421;