17-1714314-T-C

Variant summary

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

The NR_028505.1(MIR22HG):n.144-300A>G variant causes a intron, non coding transcript 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 NR_028505.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR22HG	NR_028505.1	n.144-300A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028502.1	n.144-300A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028503.1	n.144-300A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028504.1	n.226+57A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR22HG	ENST00000577164.2	n.364+57A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR exome AF: 0.675

Gnomad4 AMR exome AF: 0.708

Gnomad4 ASJ exome AF: 0.584

Gnomad4 EAS exome AF: 0.900

Gnomad4 SAS exome AF: 0.739

Gnomad4 FIN exome AF: 0.713

Gnomad4 NFE exome AF: 0.706

Gnomad4 OTH exome AF: 0.709

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

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.685

Alfa AF: 0.695 Hom.: 4437

Bravo AF: 0.709

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.6
Dann	Benign	0.61
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

Publications

LitVar

Other links and lift over

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