rs716183

Variant names:

• chr10-117144984-C-T
• rs716183
• ENST00000654523.1:n.529-251G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654523.1(MIR3663HG):​n.529-251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,034 control chromosomes in the GnomAD database, including 19,045 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 0.48 (19045 hom., cov: 32)
• Consequence: MIR3663HG ENST00000654523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

Genes affected

MIR3663HG (HGNC:50676): (MIR3663 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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
MIR3663HG	ENST00000654523.1	n.529-251G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72963 AN: 151914 Hom.: 19054 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.480 AC: 72963 AN: 152034 Hom.: 19045 Cov.: 32 AF XY: 0.483 AC XY: 35880 AN XY: 74318

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.500

Alfa AF: 0.554 Hom.: 32297

Bravo AF: 0.461

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716183; hg19: chr10-118904495;