chr1-1164939-C-A

Variant names:

• chr1-1164939-C-A
• rs1891904
• XR_007065348.1:n.1687C>A

Variant summary

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

The XR_007065348.1(MIR200BHG):​n.1687C>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 0.879 in 152,120 control chromosomes in the GnomAD database, including 59,314 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 0.88 (59314 hom., cov: 33)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	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: 133585 AN: 152002 Hom.: 59263 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.879 AC: 133690 AN: 152120 Hom.: 59314 Cov.: 33 AF XY: 0.875 AC XY: 65065 AN XY: 74372

African (AFR) AF: 0.821 AC: 34082 AN: 41488

American (AMR) AF: 0.820 AC: 12528 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3148 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2963 AN: 5132

South Asian (SAS) AF: 0.883 AC: 4263 AN: 4830

European-Finnish (FIN) AF: 0.923 AC: 9796 AN: 10616

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63887 AN: 67980

Other (OTH) AF: 0.873 AC: 1847 AN: 2116

Alfa AF: 0.910 Hom.: 9730

Bravo AF: 0.866

Asia WGS AF: 0.718 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1891904; hg19: chr1-1100319;