11-567627-G-C

Variant names:

• chr11-567627-G-C
• rs1062099
• ENST00000528245.3:n.145C>G

Variant summary

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

The ENST00000528245.3(MIR210HG):​n.145C>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 ENST00000528245.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528245.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR210HG	NR_038262.1		n.333C>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR210HG	ENST00000528245.3	TSL:3	n.145C>G		non_coding_transcript_exon	Exon 2 of 2
	MIR210HG	ENST00000533920.1	TSL:2	n.333C>G		non_coding_transcript_exon	Exon 2 of 2
	MIR210HG	ENST00000534540.3	TSL:2	n.345C>G		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.250 AC: 2 AN: 8

American (AMR) AF: 0.232 AC: 101 AN: 436

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 8 AN: 86

East Asian (EAS) AF: 0.0714 AC: 1 AN: 14

South Asian (SAS) AF: 0.0721 AC: 102 AN: 1414

European-Finnish (FIN) AF: 0.105 AC: 20 AN: 190

Middle Eastern (MID) AF: 0.125 AC: 1 AN: 8

European-Non Finnish (NFE) AF: 0.147 AC: 343 AN: 2336

Other (OTH) AF: 0.110 AC: 20 AN: 182

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

African (AFR) AF: 0.260 AC: 10779 AN: 41504

American (AMR) AF: 0.227 AC: 3472 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3472

East Asian (EAS) AF: 0.0517 AC: 268 AN: 5186

South Asian (SAS) AF: 0.0718 AC: 347 AN: 4830

European-Finnish (FIN) AF: 0.138 AC: 1466 AN: 10608

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13571 AN: 68012

Other (OTH) AF: 0.209 AC: 440 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1062099; hg19: chr11-567627;