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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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 v4.9

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;