17-7012082-C-G

Variant names:

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

Variant summary

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

The ENST00000666062.1(MIR497HG):​n.449G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 392,134 control chromosomes in the GnomAD database, including 72,031 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 0.58 (26029 hom., cov: 32)
  • Exomes 𝑓: 0.61 (46002 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX12-AS1	NR_040089.1	n.139+114G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR497HG	ENST00000666062.1	n.449G>C		non_coding_transcript_exon_variant	Exon 1 of 1
MIR497HG	ENST00000399540.3	n.154+114G>C		intron_variant	Intron 1 of 2	2
MIR497HG	ENST00000399541.7	n.155+114G>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88625 AN: 151886 Hom.: 26009 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.602

GnomAD4 exome AF: 0.612 AC: 147048 AN: 240130 Hom.: 46002 AF XY: 0.626 AC XY: 84245 AN XY: 134498

African (AFR) AF: 0.533 AC: 2939 AN: 5516

American (AMR) AF: 0.446 AC: 7479 AN: 16752

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 4928 AN: 7824

East Asian (EAS) AF: 0.532 AC: 3620 AN: 6806

South Asian (SAS) AF: 0.728 AC: 33758 AN: 46366

European-Finnish (FIN) AF: 0.584 AC: 14513 AN: 24854

Middle Eastern (MID) AF: 0.706 AC: 1670 AN: 2366

European-Non Finnish (NFE) AF: 0.603 AC: 71699 AN: 118990

Other (OTH) AF: 0.605 AC: 6442 AN: 10656

GnomAD4 genome AF: 0.583 AC: 88694 AN: 152004 Hom.: 26029 Cov.: 32 AF XY: 0.583 AC XY: 43345 AN XY: 74298

African (AFR) AF: 0.547 AC: 22660 AN: 41430

American (AMR) AF: 0.526 AC: 8042 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2852 AN: 5166

South Asian (SAS) AF: 0.730 AC: 3516 AN: 4818

European-Finnish (FIN) AF: 0.563 AC: 5939 AN: 10546

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41445 AN: 67984

Other (OTH) AF: 0.600 AC: 1264 AN: 2106

Alfa AF: 0.461 Hom.: 1238

Bravo AF: 0.573

Asia WGS AF: 0.613 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.095
DANN	Benign	0.42
PhyloP100		-3.2
PromoterAI		0.020	Neutral
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: rs2271316; hg19: chr17-6915401; COSMIC: COSV107242405;