rs17551939

Variant names:

• chr2-12128622-A-C
• rs17551939
• ENST00000412294.6:n.208-38116A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-12128622-A-C
• chr2-12128622-A-G

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.208-38116A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,826 control chromosomes in the GnomAD database, including 5,759 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 0.27 (5759 hom., cov: 31)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 2 publications found

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412294.6. 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
	MIR3681HG	NR_110196.1		n.210-38116A>C		intron	N/A
	MIR3681HG	NR_110197.1		n.344-2684A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.208-38116A>C		intron	N/A
	MIR3681HG	ENST00000438292.5	TSL:3	n.129-38116A>C		intron	N/A
	MIR3681HG	ENST00000449986.3	TSL:2	n.561-2684A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40257 AN: 151708 Hom.: 5762 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40255 AN: 151826 Hom.: 5759 Cov.: 31 AF XY: 0.260 AC XY: 19279 AN XY: 74174

African (AFR) AF: 0.197 AC: 8154 AN: 41396

American (AMR) AF: 0.206 AC: 3141 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.0700 AC: 362 AN: 5174

South Asian (SAS) AF: 0.280 AC: 1342 AN: 4798

European-Finnish (FIN) AF: 0.285 AC: 3005 AN: 10530

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22161 AN: 67930

Other (OTH) AF: 0.261 AC: 550 AN: 2106

Alfa AF: 0.285 Hom.: 1209

Bravo AF: 0.253

Asia WGS AF: 0.171 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs17551939; hg19: chr2-12268748;