chr1-1164057-G-A

Variant names:

• chr1-1164057-G-A
• rs11584885
• XR_007065348.1:n.805G>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.805G>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 0.224 in 152,084 control chromosomes in the GnomAD database, including 4,381 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 0.22 (4381 hom., cov: 32)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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: 0.224 AC: 34008 AN: 151966 Hom.: 4382 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.224 AC: 34023 AN: 152084 Hom.: 4381 Cov.: 32 AF XY: 0.223 AC XY: 16552 AN XY: 74326

African (AFR) AF: 0.156 AC: 6468 AN: 41524

American (AMR) AF: 0.148 AC: 2266 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.0296 AC: 153 AN: 5170

South Asian (SAS) AF: 0.202 AC: 974 AN: 4812

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19355 AN: 67936

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.247 Hom.: 2530

Bravo AF: 0.205

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.85
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs11584885; hg19: chr1-1099437;