rs72563729

Positions:

• chr1-1167183-G-A
• chr1-1167183-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NR_029639.1(MIR200B):​n.80G>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 0.0141 in 531,854 control chromosomes in the GnomAD database, including 94 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 0.012 (20 hom., cov: 33)
  • Exomes 𝑓: 0.015 (74 hom.)
• Consequence: MIR200B NR_029639.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511

Genes affected

MIR200B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0118 (1801/152240) while in subpopulation NFE AF= 0.0198 (1349/67974). AF 95% confidence interval is 0.019. There are 20 homozygotes in gnomad4. There are 839 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR200B	NR_029639.1	n.80G>A		non_coding_transcript_exon_variant	1/1
LOC124903818	XR_007065348.1	n.3931G>A		non_coding_transcript_exon_variant	2/2
MIR200B	unassigned_transcript_7	n.*38G>A		downstream_gene_variant
MIR200B	unassigned_transcript_8	n.*2G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR200B	ENST00000384997.3	n.80G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0118 AC: 1802 AN: 152122 Hom.: 20 Cov.: 33

Gnomad AFR AF: 0.00292

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00661

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.00773

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.00861

GnomAD3 exomes AF: 0.0127 AC: 3103 AN: 243388 Hom.: 26 AF XY: 0.0130 AC XY: 1723 AN XY: 132470

Gnomad AFR exome AF: 0.00240

Gnomad AMR exome AF: 0.00633

Gnomad ASJ exome AF: 0.00970

Gnomad EAS exome AF: 0.0000553

Gnomad SAS exome AF: 0.0154

Gnomad FIN exome AF: 0.00986

Gnomad NFE exome AF: 0.0182

Gnomad OTH exome AF: 0.0172

GnomAD4 exome AF: 0.0151 AC: 5715 AN: 379614 Hom.: 74 Cov.: 0 AF XY: 0.0156 AC XY: 3378 AN XY: 216124

Gnomad4 AFR exome AF: 0.00257

Gnomad4 AMR exome AF: 0.00673

Gnomad4 ASJ exome AF: 0.0102

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0167

Gnomad4 FIN exome AF: 0.0100

Gnomad4 NFE exome AF: 0.0190

Gnomad4 OTH exome AF: 0.0134

GnomAD4 genome AF: 0.0118 AC: 1801 AN: 152240 Hom.: 20 Cov.: 33 AF XY: 0.0113 AC XY: 839 AN XY: 74434

Gnomad4 AFR AF: 0.00291

Gnomad4 AMR AF: 0.00654

Gnomad4 ASJ AF: 0.00951

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.00773

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.00852

Alfa AF: 0.0138 Hom.: 7

Bravo AF: 0.0103

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72563729; hg19: chr1-1102563;