rs6502892

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-1714314-T-A
• chr17-1714314-T-C
• chr17-1714314-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000334146.10(MIR22HG):​n.243+57A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR22HG ENST00000334146.10 intron
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR22HG	NR_028502.2	n.82-300A>T		intron_variant	Intron 1 of 1
MIR22HG	NR_028503.2	n.82-300A>T		intron_variant	Intron 1 of 2
MIR22HG	NR_028504.2	n.164+57A>T		intron_variant	Intron 2 of 3
MIR22HG	NR_028505.2	n.82-300A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR22HG	ENST00000334146.10	n.243+57A>T		intron_variant	Intron 2 of 3	1
MIR22HG	ENST00000574306.3	n.144-300A>T		intron_variant	Intron 1 of 1	1
MIR22HG	ENST00000742908.1	n.231A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 58490 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 31642

African (AFR) AF: 0.00 AC: 0 AN: 3328

American (AMR) AF: 0.00 AC: 0 AN: 6000

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1354

East Asian (EAS) AF: 0.00 AC: 0 AN: 4880

South Asian (SAS) AF: 0.00 AC: 0 AN: 10042

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 138

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28688

Other (OTH) AF: 0.00 AC: 0 AN: 2534

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.71
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;