11-567627-G-C

Variant names:

• chr11-567627-G-C
• rs1062099
• ENST00000528245.2:n.139C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533920.1(MIR210HG):​n.333C>G 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 0.202 in 156,890 control chromosomes in the GnomAD database, including 3,431 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 0.20 (3371 hom., cov: 33)
  • Exomes 𝑓: 0.13 (60 hom.)
• Consequence: MIR210HG ENST00000533920.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

MIR210HG (HGNC:39524): (MIR210 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR210HG	NR_038262.1	n.333C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR210HG	ENST00000528245.2	n.139C>G		non_coding_transcript_exon_variant	Exon 2 of 2	3
MIR210HG	ENST00000533920.1	n.333C>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
MIR210HG	ENST00000534540.2	n.338C>G		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31075 AN: 152096 Hom.: 3369 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.128 AC: 598 AN: 4674 Hom.: 60 Cov.: 0 AF XY: 0.121 AC XY: 343 AN XY: 2824

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.232

Gnomad4 ASJ exome AF: 0.0930

Gnomad4 EAS exome AF: 0.0714

Gnomad4 SAS exome AF: 0.0721

Gnomad4 FIN exome AF: 0.105

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.204 AC: 31100 AN: 152216 Hom.: 3371 Cov.: 33 AF XY: 0.197 AC XY: 14689 AN XY: 74432

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.209

Alfa AF: 0.101 Hom.: 132

Bravo AF: 0.215

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1062099; hg19: chr11-567627;