rs11078597

Variant names:

• chr17-1715069-T-C
• rs11078597
• ENST00000334146.10:n.161-616A>G

Variant summary

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

The ENST00000334146.10(MIR22HG):​n.161-616A>G variant causes a intron 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 ENST00000334146.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 35 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=-0.72).
• 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 rank	MANE	Protein	UniProt
MIR22HG	NR_028502.2	n.82-1055A>G		intron_variant	Intron 1 of 1
MIR22HG	NR_028503.2	n.82-1055A>G		intron_variant	Intron 1 of 2
MIR22HG	NR_028504.2	n.82-616A>G		intron_variant	Intron 1 of 3
MIR22HG	NR_028505.2	n.82-1055A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR22HG	ENST00000334146.10	n.161-616A>G		intron_variant	Intron 1 of 3	1
MIR22HG	ENST00000574306.3	n.144-1055A>G		intron_variant	Intron 1 of 1	1
MIR22HG	ENST00000570416.7	n.134-1055A>G		intron_variant	Intron 1 of 2	3

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

African (AFR) AF: 0.184 AC: 7648 AN: 41488

American (AMR) AF: 0.242 AC: 3694 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3466

East Asian (EAS) AF: 0.189 AC: 978 AN: 5172

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4826

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12495 AN: 67972

Other (OTH) AF: 0.196 AC: 413 AN: 2108

Alfa AF: 0.187 Hom.: 9586

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
PhyloP100		0.23

Splicing

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

Other links and lift over

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