rs11078597

chr17-1715069-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.144-1055A>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 0.195 in 152,128 control chromosomes in the GnomAD database, including 3,030 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 (3030 hom., cov: 33)
• Consequence: MIR22HG NR_028505.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR22HG	NR_028505.1	n.144-1055A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028502.1	n.144-1055A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028503.1	n.144-1055A>G		intron_variant, non_coding_transcript_variant
MIR22HG	NR_028504.1	n.144-616A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR22HG	ENST00000577164.2	n.282-616A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29649 AN: 152010 Hom.: 3030 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.189

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.195 AC: 29665 AN: 152128 Hom.: 3030 Cov.: 33 AF XY: 0.200 AC XY: 14851 AN XY: 74396

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.196

Alfa AF: 0.187 Hom.: 3366

Bravo AF: 0.192

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	14
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11078597; hg19: chr17-1618363; COSMIC: COSV58007675;