14-27067046-A-G

Variant names:

• chr14-27067046-A-G
• rs1951758
• ENST00000552303.1:n.206-10192A>G

Variant summary

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

The ENST00000552303.1(MIR4307HG):​n.206-10192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,802 control chromosomes in the GnomAD database, including 30,467 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 0.63 (30467 hom., cov: 31)
• Consequence: MIR4307HG ENST00000552303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 2 publications found

Genes affected

MIR4307HG (HGNC:52004): (MIR4307 host gene)

NOVA1-DT (HGNC:19827): (NOVA1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552303.1. 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
	MIR4307HG	ENST00000552303.1	TSL:4	n.206-10192A>G		intron	N/A
	NOVA1-DT	ENST00000656336.1		n.481-66924A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95230 AN: 151684 Hom.: 30446 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.628 AC: 95288 AN: 151802 Hom.: 30467 Cov.: 31 AF XY: 0.627 AC XY: 46484 AN XY: 74162

African (AFR) AF: 0.590 AC: 24425 AN: 41394

American (AMR) AF: 0.710 AC: 10815 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1283 AN: 5106

South Asian (SAS) AF: 0.634 AC: 3051 AN: 4810

European-Finnish (FIN) AF: 0.677 AC: 7161 AN: 10574

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 43975 AN: 67906

Other (OTH) AF: 0.632 AC: 1332 AN: 2106

Alfa AF: 0.634 Hom.: 91991

Bravo AF: 0.623

Asia WGS AF: 0.487 AC: 1691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.86
PhyloP100		-0.14

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: rs1951758;

hg19: chr14-27536252;