chr1-1164837-C-T

Variant names:

• chr1-1164837-C-T
• rs1891905
• XR_007065348.1:n.1585C>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.1585C>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 0.885 in 152,230 control chromosomes in the GnomAD database, including 60,132 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 (60132 hom., cov: 34)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 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: 0.885 AC: 134575 AN: 152112 Hom.: 60085 Cov.: 34

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.885 AC: 134677 AN: 152230 Hom.: 60132 Cov.: 34 AF XY: 0.883 AC XY: 65715 AN XY: 74426

African (AFR) AF: 0.801 AC: 33261 AN: 41516

American (AMR) AF: 0.914 AC: 13984 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3119 AN: 5160

South Asian (SAS) AF: 0.887 AC: 4281 AN: 4824

European-Finnish (FIN) AF: 0.924 AC: 9811 AN: 10620

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63980 AN: 68012

Other (OTH) AF: 0.888 AC: 1879 AN: 2116

Alfa AF: 0.920 Hom.: 89028

Bravo AF: 0.878

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1891905; hg19: chr1-1100217;