rs716183

Variant names:

• chr10-117144984-C-T
• rs716183
• ENST00000654523.2:n.541-251G>A

Variant summary

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

The ENST00000654523.2(MIR3663HG):​n.541-251G>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 ENST00000654523.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654523.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3663HG	ENST00000654523.2		n.541-251G>A		intron	N/A
	MIR3663HG	ENST00000746790.1		n.632-514G>A		intron	N/A
	MIR3663HG	ENST00000746791.1		n.621-251G>A		intron	N/A

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

African (AFR) AF: 0.258 AC: 10690 AN: 41462

American (AMR) AF: 0.511 AC: 7798 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1879 AN: 3468

East Asian (EAS) AF: 0.556 AC: 2879 AN: 5178

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4818

European-Finnish (FIN) AF: 0.650 AC: 6859 AN: 10548

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39057 AN: 67972

Other (OTH) AF: 0.500 AC: 1055 AN: 2112

Alfa AF: 0.544 Hom.: 39380

Bravo AF: 0.461

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.23
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs716183;

hg19: chr10-118904495;