17-7012082-C-T

Variant names:

• chr17-7012082-C-T
• rs2271316
• ENST00000666062.1:n.449G>A

Variant summary

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

The ENST00000666062.1(MIR497HG):​n.449G>A variant causes a non coding transcript exon 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR497HG ENST00000666062.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21
• Publications: 23 publications found

Genes affected

MIR497HG (HGNC:39523): (mir-497-195 cluster host gene)

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666062.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX12-AS1	NR_040089.1		n.139+114G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR497HG	ENST00000666062.1		n.449G>A		non_coding_transcript_exon	Exon 1 of 1
	MIR497HG	ENST00000399540.3	TSL:2	n.154+114G>A		intron	N/A
	MIR497HG	ENST00000399541.7	TSL:2	n.155+114G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 241022 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 134960

African (AFR) AF: 0.00 AC: 0 AN: 5536

American (AMR) AF: 0.00 AC: 0 AN: 16842

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7842

East Asian (EAS) AF: 0.00 AC: 0 AN: 6836

South Asian (SAS) AF: 0.00 AC: 0 AN: 46500

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24920

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2382

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 119464

Other (OTH) AF: 0.00 AC: 0 AN: 10700

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.13
DANN	Benign	0.57
PhyloP100		-3.2
PromoterAI		-0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2271316; hg19: chr17-6915401;