chr17-6986238-G-A

Variant names:

• chr17-6986238-G-A
• rs6502998
• ENST00000399541.7:n.250-698C>T

Variant summary

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

The ENST00000399541.7(MIR497HG):​n.250-698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,840 control chromosomes in the GnomAD database, including 35,943 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 0.68 (35943 hom., cov: 31)
• Consequence: MIR497HG ENST00000399541.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 9 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399541.7. 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.234-698C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR497HG	ENST00000399541.7	TSL:2	n.250-698C>T		intron	N/A
	MIR497HG	ENST00000570562.5	TSL:3	n.237+23558C>T		intron	N/A
	MIR497HG	ENST00000572385.6	TSL:4	n.233+23558C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102957 AN: 151722 Hom.: 35882 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.679 AC: 103073 AN: 151840 Hom.: 35943 Cov.: 31 AF XY: 0.679 AC XY: 50402 AN XY: 74190

African (AFR) AF: 0.840 AC: 34798 AN: 41414

American (AMR) AF: 0.742 AC: 11320 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3468

East Asian (EAS) AF: 0.607 AC: 3120 AN: 5140

South Asian (SAS) AF: 0.546 AC: 2636 AN: 4826

European-Finnish (FIN) AF: 0.651 AC: 6852 AN: 10532

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40247 AN: 67904

Other (OTH) AF: 0.655 AC: 1380 AN: 2106

Alfa AF: 0.621 Hom.: 31181

Bravo AF: 0.694

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6502998; hg19: chr17-6889557;