chr1-1163440-TC-T

Variant names:

• chr1-1163440-TC-T
• rs5772039
• XR_007065348.1:n.383-186delC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_007065348.1(MIR200BHG):​n.383-186delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (59169 hom., cov: 0)
• Consequence: MIR200BHG XR_007065348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 0 publications found

Genes affected

MIR200BHG (HGNC:58145):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 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: 0.879 AC: 133322 AN: 151608 Hom.: 59121 Cov.: 0

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.879 AC: 133426 AN: 151724 Hom.: 59169 Cov.: 0 AF XY: 0.877 AC XY: 65046 AN XY: 74156

African (AFR) AF: 0.817 AC: 33791 AN: 41362

American (AMR) AF: 0.898 AC: 13711 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3155 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2902 AN: 5110

South Asian (SAS) AF: 0.882 AC: 4246 AN: 4814

European-Finnish (FIN) AF: 0.900 AC: 9492 AN: 10550

Middle Eastern (MID) AF: 0.945 AC: 276 AN: 292

European-Non Finnish (NFE) AF: 0.930 AC: 63107 AN: 67854

Other (OTH) AF: 0.877 AC: 1843 AN: 2102

Alfa AF: 0.880 Hom.: 1870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs5772039; hg19: chr1-1098820;