17-1714314-T-C

Variant names:

• chr17-1714314-T-C
• rs6502892
• ENST00000334146.10:n.243+57A>G

Variant summary

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

The ENST00000742908.1(MIR22HG):​n.231A>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 0.716 in 210,452 control chromosomes in the GnomAD database, including 54,346 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 0.71 (38798 hom., cov: 33)
  • Exomes 𝑓: 0.72 (15548 hom.)
• Consequence: MIR22HG ENST00000742908.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 16 publications found

Genes affected

MIR22HG (HGNC:28219): (MIR22 host gene) Predicted to act upstream of or within response to wounding. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742908.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR22HG	NR_028502.2		n.82-300A>G		intron	N/A
	MIR22HG	NR_028503.2		n.82-300A>G		intron	N/A
	MIR22HG	NR_028504.2		n.164+57A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR22HG	ENST00000334146.10	TSL:1	n.243+57A>G		intron	N/A
	MIR22HG	ENST00000574306.3	TSL:1	n.144-300A>G		intron	N/A
	MIR22HG	ENST00000742908.1		n.231A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108389 AN: 151992 Hom.: 38760 Cov.: 33

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.680

GnomAD4 exome AF: 0.723 AC: 42210 AN: 58342 Hom.: 15548 AF XY: 0.725 AC XY: 22881 AN XY: 31572

African (AFR) AF: 0.675 AC: 2243 AN: 3322

American (AMR) AF: 0.708 AC: 4235 AN: 5980

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 788 AN: 1350

East Asian (EAS) AF: 0.900 AC: 4389 AN: 4876

South Asian (SAS) AF: 0.739 AC: 7398 AN: 10016

European-Finnish (FIN) AF: 0.713 AC: 1082 AN: 1518

Middle Eastern (MID) AF: 0.594 AC: 82 AN: 138

European-Non Finnish (NFE) AF: 0.706 AC: 20199 AN: 28612

Other (OTH) AF: 0.709 AC: 1794 AN: 2530

GnomAD4 genome AF: 0.713 AC: 108480 AN: 152110 Hom.: 38798 Cov.: 33 AF XY: 0.715 AC XY: 53176 AN XY: 74348

African (AFR) AF: 0.700 AC: 29021 AN: 41476

American (AMR) AF: 0.711 AC: 10868 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4638 AN: 5170

South Asian (SAS) AF: 0.754 AC: 3639 AN: 4828

European-Finnish (FIN) AF: 0.721 AC: 7627 AN: 10584

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48310 AN: 67994

Other (OTH) AF: 0.685 AC: 1442 AN: 2106

Alfa AF: 0.401 Hom.: 4437

Bravo AF: 0.709

Asia WGS AF: 0.833 AC: 2895 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	7.6
DANN	Benign	0.61
PhyloP100		-0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs6502892; hg19: chr17-1617608; COSMIC: COSV58007665;