Variant 17-1715069-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000334146.9(MIR22HG):n.154-616A>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
ENST00000334146.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230

Variant links:

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]

MIR22HG links:

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ACMG classification

Classification made for transcript

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	Effect
MIR22HG	NR_028502.2 link	n.82-1055A>G	intron_variant
MIR22HG	NR_028503.2 link	n.82-1055A>G	intron_variant
MIR22HG	NR_028504.2 link	n.82-616A>G	intron_variant
MIR22HG	NR_028505.2 link	n.82-1055A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR22HG	ENST00000334146.9 link	n.154-616A>G	intron_variant	1
MIR22HG	ENST00000574306.2 link	n.123-1055A>G	intron_variant	1
MIR22HG	ENST00000570416.6 link	n.107-1055A>G	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29649

AN:

152010

Hom.:

3030

Cov.:

show subpopulations

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.:

AF XY:

0.200

AC XY:

14851

AN XY:

74396

show subpopulations

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

DANN

Benign

0.66

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over