rs6502997

Variant names:

• chr17-6984439-A-C
• rs6502997
• ENST00000570562.5:n.237+25357T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-6984439-A-C
• chr17-6984439-A-T

Variant summary

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

The ENST00000570562.5(MIR497HG):​n.237+25357T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,008 control chromosomes in the GnomAD database, including 32,663 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 0.65 (32663 hom., cov: 33)
• Consequence: MIR497HG ENST00000570562.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 20 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR497HG	ENST00000570562.5	n.237+25357T>G		intron_variant	Intron 2 of 3	3
MIR497HG	ENST00000572385.6	n.233+25357T>G		intron_variant	Intron 2 of 4	4
MIR497HG	ENST00000575889.5	n.216+25357T>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99269 AN: 151890 Hom.: 32640 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.653 AC: 99332 AN: 152008 Hom.: 32663 Cov.: 33 AF XY: 0.649 AC XY: 48202 AN XY: 74306

African (AFR) AF: 0.697 AC: 28901 AN: 41462

American (AMR) AF: 0.537 AC: 8191 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2435 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3600 AN: 5168

South Asian (SAS) AF: 0.664 AC: 3201 AN: 4822

European-Finnish (FIN) AF: 0.592 AC: 6253 AN: 10556

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44574 AN: 67948

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.641 Hom.: 25229

Bravo AF: 0.646

Asia WGS AF: 0.660 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.1
DANN	Benign	0.95
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6502997; hg19: chr17-6887758;