rs11907714

Variant names:

• chr20-60221559-A-G
• rs11907714
• ENST00000421257.1:n.35+40646A>G

Variant summary

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

The ENST00000432910.5(MIR646HG):​n.332+40646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,202 control chromosomes in the GnomAD database, including 4,664 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 0.20 (4664 hom., cov: 33)
• Consequence: MIR646HG ENST00000432910.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 3 publications found

Genes affected

MIR646HG (HGNC:27659): (MIR646 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 (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432910.5. 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
	MIR646HG	NR_046099.1		n.332+40646A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000421257.1	TSL:3	n.35+40646A>G		intron	N/A
	MIR646HG	ENST00000427820.1	TSL:5	n.27-25234A>G		intron	N/A
	MIR646HG	ENST00000431181.5	TSL:3	n.767-24479A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29681 AN: 152084 Hom.: 4638 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.195 AC: 29755 AN: 152202 Hom.: 4664 Cov.: 33 AF XY: 0.196 AC XY: 14597 AN XY: 74426

African (AFR) AF: 0.441 AC: 18264 AN: 41458

American (AMR) AF: 0.120 AC: 1841 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3470

East Asian (EAS) AF: 0.0572 AC: 297 AN: 5192

South Asian (SAS) AF: 0.0988 AC: 477 AN: 4830

European-Finnish (FIN) AF: 0.173 AC: 1835 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6171 AN: 68014

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.117 Hom.: 2816

Bravo AF: 0.203

Asia WGS AF: 0.121 AC: 420 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	0.56
DANN	Benign	0.78
PhyloP100		-0.39
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: rs11907714; hg19: chr20-58796617;